diff --git a/package-lock.json b/package-lock.json
index 6e0bc60ef577f..bb5ce7fe255b7 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -8,6 +8,9 @@
             "name": "typescript",
             "version": "6.0.0",
             "license": "Apache-2.0",
+            "dependencies": {
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+            },
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                 "tsc": "bin/tsc",
                 "tsserver": "bin/tsserver"
@@ -61,6 +64,112 @@
                 "node": ">=14.17"
             }
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+            "resolved": "https://registry.npmjs.org/@andrewbranch/ts-fix-baseurl/-/ts-fix-baseurl-1.0.9.tgz",
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+            "license": "MIT",
+            "dependencies": {
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+                "glob": "^11.0.3"
+            },
+            "bin": {
+                "ts-fix-baseurl": "dist/cli.js"
+            },
+            "engines": {
+                "node": ">=20.19.0"
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+        "node_modules/@andrewbranch/ts-fix-baseurl/node_modules/chalk": {
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+            "resolved": "https://registry.npmjs.org/chalk/-/chalk-5.6.2.tgz",
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+            "license": "MIT",
+            "engines": {
+                "node": "^12.17.0 || ^14.13 || >=16.0.0"
+            },
+            "funding": {
+                "url": "https://github.com/chalk/chalk?sponsor=1"
+            }
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+            "license": "ISC",
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+                "glob": "dist/esm/bin.mjs"
+            },
+            "engines": {
+                "node": "20 || >=22"
+            },
+            "funding": {
+                "url": "https://github.com/sponsors/isaacs"
+            }
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+            "license": "BlueOak-1.0.0",
+            "dependencies": {
+                "@isaacs/cliui": "^8.0.2"
+            },
+            "engines": {
+                "node": "20 || >=22"
+            },
+            "funding": {
+                "url": "https://github.com/sponsors/isaacs"
+            }
+        },
+        "node_modules/@andrewbranch/ts-fix-baseurl/node_modules/lru-cache": {
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+            "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-11.2.1.tgz",
+            "integrity": "sha512-r8LA6i4LP4EeWOhqBaZZjDWwehd1xUJPCJd9Sv300H0ZmcUER4+JPh7bqqZeqs1o5pgtgvXm+d9UGrB5zZGDiQ==",
+            "license": "ISC",
+            "engines": {
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+            }
+        },
+        "node_modules/@andrewbranch/ts-fix-baseurl/node_modules/minimatch": {
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+            "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-10.0.3.tgz",
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+            "license": "ISC",
+            "dependencies": {
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+            },
+            "engines": {
+                "node": "20 || >=22"
+            },
+            "funding": {
+                "url": "https://github.com/sponsors/isaacs"
+            }
+        },
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+            "resolved": "https://registry.npmjs.org/path-scurry/-/path-scurry-2.0.0.tgz",
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+            "license": "BlueOak-1.0.0",
+            "dependencies": {
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+                "minipass": "^7.1.2"
+            },
+            "engines": {
+                "node": "20 || >=22"
+            },
+            "funding": {
+                "url": "https://github.com/sponsors/isaacs"
+            }
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@@ -908,11 +1017,31 @@
                 "url": "https://github.com/sponsors/nzakas"
             }
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+        "node_modules/@isaacs/balanced-match": {
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+            "resolved": "https://registry.npmjs.org/@isaacs/balanced-match/-/balanced-match-4.0.1.tgz",
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+            "license": "MIT",
+            "engines": {
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+            }
+        },
+        "node_modules/@isaacs/brace-expansion": {
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+            "license": "MIT",
+            "dependencies": {
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             },
@@ -8437,8 +8581,7 @@
                 "ansi-regex": {
                     "version": "5.0.1",
                     "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.1.tgz",
-                    "integrity": "sha512-quJQXlTSUGL2LH9SUXo8VwsY4soanhgo6LNSm84E1LBcE8s3O0wpdiRzyR9z/ZZJMlMWv37qOOb9pdJlMUEKFQ==",
-                    "dev": true
+                    "integrity": "sha512-quJQXlTSUGL2LH9SUXo8VwsY4soanhgo6LNSm84E1LBcE8s3O0wpdiRzyR9z/ZZJMlMWv37qOOb9pdJlMUEKFQ=="
                 }
             }
         },
@@ -8645,7 +8788,6 @@
             "version": "8.1.0",
             "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-8.1.0.tgz",
             "integrity": "sha512-si7QWI6zUMq56bESFvagtmzMdGOtoxfR+Sez11Mobfc7tm+VkUckk9bW2UeffTGVUbOksxmSw0AA2gs8g71NCQ==",
-            "dev": true,
             "requires": {
                 "ansi-styles": "^6.1.0",
                 "string-width": "^5.0.1",
@@ -8655,8 +8797,7 @@
                 "ansi-styles": {
                     "version": "6.2.1",
                     "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-6.2.1.tgz",
-                    "integrity": "sha512-bN798gFfQX+viw3R7yrGWRqnrN2oRkEkUjjl4JNn4E8GxxbjtG3FbrEIIY3l8/hrwUwIeCZvi4QuOTP4MErVug==",
-                    "dev": true
+                    "integrity": "sha512-bN798gFfQX+viw3R7yrGWRqnrN2oRkEkUjjl4JNn4E8GxxbjtG3FbrEIIY3l8/hrwUwIeCZvi4QuOTP4MErVug=="
                 }
             }
         },
@@ -8664,7 +8805,6 @@
             "version": "npm:wrap-ansi@7.0.0",
             "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz",
             "integrity": "sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==",
-            "dev": true,
             "requires": {
                 "ansi-styles": "^4.0.0",
                 "string-width": "^4.1.0",
@@ -8674,20 +8814,17 @@
                 "ansi-regex": {
                     "version": "5.0.1",
                     "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.1.tgz",
-                    "integrity": "sha512-quJQXlTSUGL2LH9SUXo8VwsY4soanhgo6LNSm84E1LBcE8s3O0wpdiRzyR9z/ZZJMlMWv37qOOb9pdJlMUEKFQ==",
-                    "dev": true
+                    "integrity": "sha512-quJQXlTSUGL2LH9SUXo8VwsY4soanhgo6LNSm84E1LBcE8s3O0wpdiRzyR9z/ZZJMlMWv37qOOb9pdJlMUEKFQ=="
                 },
                 "emoji-regex": {
                     "version": "8.0.0",
                     "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz",
-                    "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==",
-                    "dev": true
+                    "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A=="
                 },
                 "string-width": {
                     "version": "4.2.3",
                     "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz",
                     "integrity": "sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g==",
-                    "dev": true,
                     "requires": {
                         "emoji-regex": "^8.0.0",
                         "is-fullwidth-code-point": "^3.0.0",
@@ -8698,7 +8835,6 @@
                     "version": "6.0.1",
                     "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz",
                     "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==",
-                    "dev": true,
                     "requires": {
                         "ansi-regex": "^5.0.1"
                     }
diff --git a/package.json b/package.json
index ad629ace064c5..5d60b54b2fd4b 100644
--- a/package.json
+++ b/package.json
@@ -114,5 +114,8 @@
     "volta": {
         "node": "20.1.0",
         "npm": "8.19.4"
+    },
+    "dependencies": {
+        "@andrewbranch/ts-fix-baseurl": "^1.0.9"
     }
 }
diff --git a/src/compiler/executeCommandLine.ts b/src/compiler/executeCommandLine.ts
index edeb0eb277c57..bb22395b570da 100644
--- a/src/compiler/executeCommandLine.ts
+++ b/src/compiler/executeCommandLine.ts
@@ -1,3 +1,4 @@
+import { fixBaseURLSync } from "@andrewbranch/ts-fix-baseurl";
 import {
     arrayFrom,
     BuilderProgram,
@@ -613,6 +614,17 @@ function executeCommandLineWorker(
                 return sys.exit(ExitStatus.DiagnosticsPresent_OutputsSkipped);
             }
         }
+
+        const fixBaseURLLogs: string[] = [];
+        try {
+            const fixes = fixBaseURLSync(configFileName, log => fixBaseURLLogs.push(log));
+            for (const [fileName, text] of Object.entries(fixes)) {
+                sys.writeFile(fileName, text);
+            }
+        }
+        catch (e) {
+            throw new Error([...fixBaseURLLogs, `Error: ${e instanceof Error ? e.message : e}`].join(sys.newLine));
+        }
     }
     else if (commandLine.fileNames.length === 0) {
         const searchPath = normalizePath(sys.getCurrentDirectory());
@@ -746,6 +758,18 @@ export function executeCommandLine(
 ): void | SolutionBuilder<EmitAndSemanticDiagnosticsBuilderProgram> | WatchOfConfigFile<EmitAndSemanticDiagnosticsBuilderProgram> {
     if (isBuildCommand(commandLineArgs)) {
         const { buildOptions, watchOptions, projects, errors } = parseBuildCommand(commandLineArgs);
+        const fixBaseURLLogs: string[] = [];
+        try {
+            for (const project of projects) {
+                const fixes = fixBaseURLSync(project, log => fixBaseURLLogs.push(log));
+                for (const [fileName, text] of Object.entries(fixes)) {
+                    sys.writeFile(fileName, text);
+                }
+            }
+        }
+        catch (e) {
+            throw new Error([...fixBaseURLLogs, `Error: ${e instanceof Error ? e.message : e}`].join(system.newLine));
+        }
         if (buildOptions.generateCpuProfile && system.enableCPUProfiler) {
             system.enableCPUProfiler(buildOptions.generateCpuProfile, () =>
                 performBuild(
diff --git a/src/compiler/program.ts b/src/compiler/program.ts
index bdfb8d0151bd7..2d6987f6c4332 100644
--- a/src/compiler/program.ts
+++ b/src/compiler/program.ts
@@ -4529,6 +4529,9 @@ export function createProgram(_rootNamesOrOptions: readonly string[] | CreatePro
             if (options.moduleResolution === ModuleResolutionKind.Node10) {
                 createDeprecatedDiagnostic("moduleResolution", "node10");
             }
+            if (options.baseUrl !== undefined) {
+                createDeprecatedDiagnostic("baseUrl");
+            }
         });
     }