diff --git a/src/ghidra/GhidraInstallation.test.ts b/src/ghidra/GhidraInstallation.test.ts
index 18f45e26be..3c6d46354c 100644
--- a/src/ghidra/GhidraInstallation.test.ts
+++ b/src/ghidra/GhidraInstallation.test.ts
@@ -1,5 +1,6 @@
 import { describe, expect, it } from "vitest";
 
+import { projectGhidraDoctorInspection } from "./GhidraDoctor.js";
 import {
   ghidraJavaEnvironment,
   inspectGhidraInstallation,
@@ -378,3 +379,47 @@ describe("Ghidra release line and JDK bounds", () => {
     ).toMatchObject({ status: "available", javaVersion: "17.0.20.1" });
   });
 });
+
+describe("Ghidra configuration paths", () => {
+  it.each([
+    [{ installDir: "./ghidra" }, "GHIDRA_INSTALL_DIR must be absolute"],
+    [{ installDir: INSTALL, javaHome: "./jdk" }, "JAVA_HOME must be absolute"],
+    [
+      { installDir: "ghidra", javaHome: "jdk" },
+      "GHIDRA_INSTALL_DIR and JAVA_HOME must be absolute",
+    ],
+  ])(
+    "rejects relative paths that REA's configuration parser rejects (%o)",
+    (paths, detail) => {
+      const result = inspectGhidraInstallation(
+        { ...paths, platform: "linux", architecture: "x64" },
+        host(),
+      );
+      expect(result).toMatchObject({
+        status: "unavailable",
+        rejection: {
+          code: "not_configured",
+          reason: expect.stringContaining("reject relative paths"),
+        },
+      });
+      expect(result.checks).toContainEqual(
+        expect.objectContaining({ name: "configuration", detail }),
+      );
+      // Setup registers only an available inspection's environment.
+      expect(projectGhidraDoctorInspection(result)).toMatchObject({
+        available: false,
+        registrationEnvironment: {},
+      });
+    },
+  );
+
+  it("judges absolute paths by the inspected platform", () => {
+    const result = inspectGhidraInstallation(
+      { installDir: "C:\\ghidra", platform: "win32", architecture: "x64" },
+      host(),
+    );
+    expect(result.checks).toContainEqual(
+      expect.objectContaining({ name: "configuration", status: "passed" }),
+    );
+  });
+});
diff --git a/src/ghidra/GhidraInstallation.ts b/src/ghidra/GhidraInstallation.ts
index a521fc171b..d0906fb527 100644
--- a/src/ghidra/GhidraInstallation.ts
+++ b/src/ghidra/GhidraInstallation.ts
@@ -306,13 +306,7 @@ const installationChecks = ({
   javaHome,
   host,
 }: GhidraInstallationCheckContext): readonly GhidraInstallationCheck[] => [
-  installationCheck({
-    name: "configuration",
-    passed: coordinates.installDir !== null,
-    code: "not_configured",
-    detail: coordinates.installDir ?? "GHIDRA_INSTALL_DIR is not set",
-    remediation: `Set GHIDRA_INSTALL_DIR to an extracted Ghidra ${ghidraReleaseLine()} release directory.`,
-  }),
+  configurationCheck(coordinates.installDir, javaHome, platform),
   installationCheck({
     name: "platform",
     passed: NATIVE_PLATFORMS[platform] !== undefined,
@@ -366,6 +360,40 @@ const installationChecks = ({
   ),
 ];
 
+/**
+ * REA's configuration parser, and so the MCP server and analysis, accept only
+ * absolute paths; a relative one that happens to resolve here must not pass.
+ */
+const configurationCheck = (
+  installDir: string | null,
+  javaHome: string | undefined,
+  platform: NodeJS.Platform,
+): GhidraInstallationCheck => {
+  const { isAbsolute } = platform === "win32" ? win32 : posix;
+  const relative = [
+    ...(installDir !== null && !isAbsolute(installDir)
+      ? ["GHIDRA_INSTALL_DIR"]
+      : []),
+    ...(javaHome !== undefined && !isAbsolute(javaHome) ? ["JAVA_HOME"] : []),
+  ];
+  if (installDir === null || relative.length === 0)
+    return installationCheck({
+      name: "configuration",
+      passed: installDir !== null,
+      code: "not_configured",
+      detail: installDir ?? "GHIDRA_INSTALL_DIR is not set",
+      remediation: `Set GHIDRA_INSTALL_DIR to an extracted Ghidra ${ghidraReleaseLine()} release directory.`,
+    });
+  const settings = relative.join(" and ");
+  return installationCheck({
+    name: "configuration",
+    passed: false,
+    code: "not_configured",
+    detail: `${settings} must be absolute`,
+    remediation: `Set ${settings} to ${relative.length === 1 ? "an absolute path" : "absolute paths"}. REA's analysis and MCP server reject relative paths even when they resolve from the current directory.`,
+  });
+};
+
 /** Project an installation probe into caller-visible, secret-free diagnostics. */
 export const ghidraInstallationDiagnostics = (
   inspection: GhidraInstallationInspection,