diff --git a/.env.example b/.env.example
index 36f86f3..f42c4eb 100644
--- a/.env.example
+++ b/.env.example
@@ -18,3 +18,8 @@ API_PORT=8000
 
 # CORS — comma-separated list of allowed origins
 CORS_ORIGINS=http://localhost:3000,http://localhost:8000
+
+# App API bearer token — gates /api/app/* (companion app + scheduler).
+# Distinct from any MCP token. Generate with: python -m scripts.generate_token
+# Leave unset in dev to skip auth (a startup warning will be logged).
+# BRAIN3_APP_BEARER_TOKEN=
diff --git a/app/auth.py b/app/auth.py
new file mode 100644
index 0000000..849cea6
--- /dev/null
+++ b/app/auth.py
@@ -0,0 +1,92 @@
+# BRAIN 3.0 — AI-powered personal operating system for ADHD
+# Copyright (C) 2026 L (WilliM233)
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+"""Bearer token authentication for the App API surface (``/api/app/*``).
+
+Mirrors the pattern in ``brain3-mcp/mcp/auth.py``: a Starlette
+``BaseHTTPMiddleware`` that validates ``Authorization: Bearer <token>`` using
+``hmac.compare_digest`` for constant-time comparison.
+
+Scoped by path prefix so the existing ``/api/*`` surface (consumed by
+``brain3-mcp`` and other internal clients) remains unauthenticated. Only
+requests under ``/api/app/`` are gated. The token is sourced from
+``settings.APP_BEARER_TOKEN`` (env var ``BRAIN3_APP_BEARER_TOKEN``) and is
+intentionally distinct from any MCP token — separate secrets, separate
+rotation.
+"""
+
+from __future__ import annotations
+
+import hmac
+import logging
+
+from fastapi import FastAPI
+from starlette.middleware.base import BaseHTTPMiddleware
+from starlette.requests import Request
+from starlette.responses import JSONResponse, Response
+
+logger = logging.getLogger(__name__)
+
+APP_PATH_PREFIX = "/api/app/"
+
+
+class AppBearerAuthMiddleware(BaseHTTPMiddleware):
+    """Bearer auth on ``/api/app/*``. Pass-through for all other paths.
+
+    Token comparison uses ``hmac.compare_digest`` to prevent timing attacks
+    against the shared secret.
+    """
+
+    def __init__(self, app, token: str) -> None:
+        super().__init__(app)
+        self.token = token
+
+    async def dispatch(self, request: Request, call_next) -> Response:
+        if not request.url.path.startswith(APP_PATH_PREFIX):
+            return await call_next(request)
+
+        auth_header = request.headers.get("authorization", "")
+        if not auth_header.startswith("Bearer "):
+            return JSONResponse(
+                {"error": "Missing bearer token"}, status_code=401,
+            )
+
+        provided = auth_header[len("Bearer ") :]
+        if not hmac.compare_digest(provided, self.token):
+            return JSONResponse(
+                {"error": "Invalid bearer token"}, status_code=401,
+            )
+
+        return await call_next(request)
+
+
+def install_app_bearer_auth(app: FastAPI, token: str | None) -> None:
+    """Mount :class:`AppBearerAuthMiddleware` if ``token`` is set.
+
+    When ``token`` is ``None`` or empty, the middleware is **not** mounted
+    and a startup warning is logged. This matches the existing graceful-
+    degradation pattern used elsewhere in the app and lets local dev work
+    without forcing a token in ``.env``. Production deployments must set
+    ``BRAIN3_APP_BEARER_TOKEN`` before exposing the app API.
+    """
+    if not token:
+        logger.warning(
+            "BRAIN3_APP_BEARER_TOKEN is not set — /api/app/* endpoints are "
+            "UNAUTHENTICATED. Set the env var to enable bearer auth before "
+            "exposing the app API.",
+        )
+        return
+    app.add_middleware(AppBearerAuthMiddleware, token=token)
diff --git a/app/config.py b/app/config.py
index 44b22e9..ef241a6 100644
--- a/app/config.py
+++ b/app/config.py
@@ -16,6 +16,7 @@
 
 """Application configuration via Pydantic Settings."""
 
+from pydantic import Field
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
 
@@ -33,7 +34,16 @@ class Settings(BaseSettings):
 
     CORS_ORIGINS: str = "http://localhost:3000,http://localhost:8000"
 
-    model_config = SettingsConfigDict(env_file=".env", env_file_encoding="utf-8")
+    # Shared-secret bearer token gating /api/app/* (companion app + scheduler).
+    # Distinct from any MCP token. Unset in dev → middleware skipped with a
+    # startup warning. Required in production.
+    APP_BEARER_TOKEN: str | None = Field(
+        default=None, validation_alias="BRAIN3_APP_BEARER_TOKEN",
+    )
+
+    model_config = SettingsConfigDict(
+        env_file=".env", env_file_encoding="utf-8", populate_by_name=True,
+    )
 
     @property
     def database_url(self) -> str:
diff --git a/app/main.py b/app/main.py
index f531284..bc4f357 100644
--- a/app/main.py
+++ b/app/main.py
@@ -21,6 +21,7 @@
 from fastapi.responses import JSONResponse
 from sqlalchemy import text
 
+from app.auth import install_app_bearer_auth
 from app.config import settings
 from app.database import SessionLocal
 from app.routers import (
@@ -57,6 +58,10 @@
     allow_headers=["*"],
 )
 
+# Bearer auth on /api/app/*. Skipped with a warning when the token is unset
+# (dev convenience) — production must set BRAIN3_APP_BEARER_TOKEN.
+install_app_bearer_auth(app, settings.APP_BEARER_TOKEN)
+
 
 @app.get("/health")
 def health_check() -> dict:
@@ -75,6 +80,17 @@ def health_check() -> dict:
         )
 
 
+@app.get("/api/app/health")
+def app_health_check() -> dict:
+    """Authed probe endpoint for the companion app's validation ping.
+
+    Sits behind ``AppBearerAuthMiddleware``. The companion app calls this
+    during URL+token pairing to confirm both that the server is reachable
+    and that the bearer token is valid.
+    """
+    return {"ok": True}
+
+
 app.include_router(domains.router, prefix="/api/domains", tags=["Domains"])
 app.include_router(goals.router, prefix="/api/goals", tags=["Goals"])
 app.include_router(projects.router, prefix="/api/projects", tags=["Projects"])
diff --git a/scripts/generate_token.py b/scripts/generate_token.py
new file mode 100644
index 0000000..a1d4fe8
--- /dev/null
+++ b/scripts/generate_token.py
@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+# BRAIN 3.0 — AI-powered personal operating system for ADHD
+# Copyright (C) 2026 L (WilliM233)
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+"""Generate a BRAIN 3.0 app-API bearer token.
+
+Prints a URL-safe 48-byte random token to stdout. The companion app and the
+scheduler authenticate to ``/api/app/*`` with this token, so it should be
+treated as a shared secret. After generating, set::
+
+    BRAIN3_APP_BEARER_TOKEN=<value>
+
+in the ``.env`` file (or your deployment secret store), then restart the API.
+
+The token is the shared secret itself — there is no DB write, no user
+record, no per-device state. Rotation = generate a new token, update the
+env, restart the API. (Per-device tokens and rotation tooling are Phase 3.)
+
+Usage:
+    python -m scripts.generate_token
+"""
+
+from __future__ import annotations
+
+import secrets
+import sys
+
+TOKEN_BYTES = 48
+
+
+def main() -> None:
+    """Print a fresh URL-safe token to stdout, with a hint to stderr."""
+    token = secrets.token_urlsafe(TOKEN_BYTES)
+    # Token-only on stdout so it captures cleanly:
+    #     TOKEN=$(python -m scripts.generate_token)
+    print(token)
+    # Operator hint goes to stderr so it doesn't pollute the captured value.
+    print(
+        f"Set BRAIN3_APP_BEARER_TOKEN={token} in your .env file "
+        "(or secret store) and restart the API to enable /api/app/* auth.",
+        file=sys.stderr,
+    )
+
+
+if __name__ == "__main__":
+    main()
diff --git a/tests/test_app_auth.py b/tests/test_app_auth.py
new file mode 100644
index 0000000..3b7a63d
--- /dev/null
+++ b/tests/test_app_auth.py
@@ -0,0 +1,146 @@
+# BRAIN 3.0 — AI-powered personal operating system for ADHD
+# Copyright (C) 2026 L (WilliM233)
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+"""Tests for the App API bearer-token middleware (``app/auth.py``).
+
+Covers the four acceptance paths from issue #200 — missing header, wrong
+token, correct token, env-unset warning — plus the no-regression check that
+non-``/api/app/*`` routes stay unauthenticated when the middleware is on.
+
+Each test builds its own ``FastAPI`` app rather than reusing the global
+``app.main.app``: that app's middleware is wired up at import time from the
+real env, so per-test scenarios (no-token, known-token) need a clean
+instance.
+"""
+
+from __future__ import annotations
+
+import logging
+
+import pytest
+from fastapi import FastAPI
+from fastapi.testclient import TestClient
+
+from app.auth import AppBearerAuthMiddleware, install_app_bearer_auth
+
+TEST_TOKEN = "test-bearer-token-abc123"  # noqa: S105 — fixture, not a real secret
+
+
+def _app_with_token(token: str) -> FastAPI:
+    """Build a fresh app with the middleware mounted to ``token``."""
+    fresh = FastAPI()
+    fresh.add_middleware(AppBearerAuthMiddleware, token=token)
+
+    @fresh.get("/api/app/health")
+    def app_health() -> dict:
+        return {"ok": True}
+
+    @fresh.get("/api/notifications/ping")
+    def notif_ping() -> dict:
+        return {"pong": True}
+
+    return fresh
+
+
+@pytest.fixture
+def authed_client() -> TestClient:
+    """TestClient against a fresh app with the bearer middleware enabled."""
+    return TestClient(_app_with_token(TEST_TOKEN))
+
+
+# ---------------------------------------------------------------------------
+# Acceptance paths — issue #200
+# ---------------------------------------------------------------------------
+
+def test_missing_authorization_header_returns_401(authed_client: TestClient) -> None:
+    """No Authorization header → 401 with the missing-token error body."""
+    resp = authed_client.get("/api/app/health")
+    assert resp.status_code == 401
+    assert resp.json() == {"error": "Missing bearer token"}
+
+
+def test_wrong_token_returns_401(authed_client: TestClient) -> None:
+    """Authorization header with the wrong secret → 401 invalid-token."""
+    resp = authed_client.get(
+        "/api/app/health",
+        headers={"Authorization": "Bearer not-the-real-token"},
+    )
+    assert resp.status_code == 401
+    assert resp.json() == {"error": "Invalid bearer token"}
+
+
+def test_correct_token_returns_200(authed_client: TestClient) -> None:
+    """Authorization header with the right secret → endpoint runs."""
+    resp = authed_client.get(
+        "/api/app/health",
+        headers={"Authorization": f"Bearer {TEST_TOKEN}"},
+    )
+    assert resp.status_code == 200
+    assert resp.json() == {"ok": True}
+
+
+def test_unset_token_emits_warning_and_skips_middleware(
+    caplog: pytest.LogCaptureFixture,
+) -> None:
+    """``install_app_bearer_auth`` warns and stays a no-op when token is unset."""
+    fresh = FastAPI()
+
+    @fresh.get("/api/app/health")
+    def app_health() -> dict:
+        return {"ok": True}
+
+    with caplog.at_level(logging.WARNING, logger="app.auth"):
+        install_app_bearer_auth(fresh, None)
+
+    assert any(
+        "BRAIN3_APP_BEARER_TOKEN is not set" in record.message
+        and record.levelno == logging.WARNING
+        for record in caplog.records
+    ), f"Expected unset-token warning; got: {[r.message for r in caplog.records]}"
+
+    # Middleware was not mounted: the endpoint serves without an auth header.
+    with TestClient(fresh) as client:
+        resp = client.get("/api/app/health")
+    assert resp.status_code == 200
+    assert resp.json() == {"ok": True}
+
+
+# ---------------------------------------------------------------------------
+# Regression — issue #200: existing /api/* routes stay unauthenticated
+# ---------------------------------------------------------------------------
+
+def test_non_app_paths_pass_through_when_middleware_active(
+    authed_client: TestClient,
+) -> None:
+    """Routes outside ``/api/app/*`` are not gated even with the middleware on.
+
+    Guards the no-regression criterion: ``/api/notifications/*`` (and every
+    other existing route consumed by MCP / internal clients) must still
+    answer without an Authorization header.
+    """
+    resp = authed_client.get("/api/notifications/ping")
+    assert resp.status_code == 200
+    assert resp.json() == {"pong": True}
+
+
+def test_empty_bearer_value_returns_401(authed_client: TestClient) -> None:
+    """Header present but value empty → still missing-token (no Bearer prefix)."""
+    resp = authed_client.get(
+        "/api/app/health",
+        headers={"Authorization": ""},
+    )
+    assert resp.status_code == 401
+    assert resp.json() == {"error": "Missing bearer token"}