diff --git a/Help/manual/cmake-file-api.7.rst b/Help/manual/cmake-file-api.7.rst
index 5f16a8b47e..a6d2345f35 100644
--- a/Help/manual/cmake-file-api.7.rst
+++ b/Help/manual/cmake-file-api.7.rst
@@ -1094,7 +1094,9 @@ with members:
 
   ``baseDirectories``
     A JSON array of strings specifying the base directories containing sources
-    in the file set.
+    in the file set.  If the file is inside the top-level source directory
+    then the path is specified relative to that directory.  Otherwise the path
+    is absolute.
 
   This field was added in codemodel version 2.5.
 
diff --git a/Source/cmFileAPICodemodel.cxx b/Source/cmFileAPICodemodel.cxx
index 280ebb0136..53efb0deb2 100644
--- a/Source/cmFileAPICodemodel.cxx
+++ b/Source/cmFileAPICodemodel.cxx
@@ -1636,7 +1636,7 @@ Json::Value Target::DumpFileSet(cmFileSet const* fs,
 
   Json::Value baseDirs = Json::arrayValue;
   for (auto const& directory : directories) {
-    baseDirs.append(directory);
+    baseDirs.append(RelativeIfUnder(this->TopSource, directory));
   }
   fileSet["baseDirectories"] = baseDirs;
 
diff --git a/Tests/RunCMake/FileAPI/codemodel-v2-data/targets/c_headers_1.json b/Tests/RunCMake/FileAPI/codemodel-v2-data/targets/c_headers_1.json
index f6cfa9c751..8d1d219014 100644
--- a/Tests/RunCMake/FileAPI/codemodel-v2-data/targets/c_headers_1.json
+++ b/Tests/RunCMake/FileAPI/codemodel-v2-data/targets/c_headers_1.json
@@ -10,25 +10,25 @@
       "name": "HEADERS",
       "type": "HEADERS",
       "visibility": "PUBLIC",
-      "baseDirectories": [".*/Tests/RunCMake/FileAPI/fileset$"]
+      "baseDirectories": ["^fileset$"]
     },
     {
       "name": "a",
       "type": "HEADERS",
       "visibility": "PRIVATE",
-      "baseDirectories": [".*/Tests/RunCMake/FileAPI/fileset$"]
+      "baseDirectories": ["^fileset$"]
     },
     {
       "name": "b",
       "type": "HEADERS",
       "visibility": "PUBLIC",
-      "baseDirectories": [".*/Tests/RunCMake/FileAPI/fileset/dir$"]
+      "baseDirectories": ["^fileset/dir$"]
     },
     {
       "name": "c",
       "type": "HEADERS",
       "visibility": "INTERFACE",
-      "baseDirectories": [".*/Tests/RunCMake/FileAPI/fileset$"]
+      "baseDirectories": ["^fileset$"]
     }
   ],
   "sources": [
diff --git a/Tests/RunCMake/FileAPI/codemodel-v2-data/targets/c_headers_2.json b/Tests/RunCMake/FileAPI/codemodel-v2-data/targets/c_headers_2.json
index 591ba4f8eb..e97f6d49b2 100644
--- a/Tests/RunCMake/FileAPI/codemodel-v2-data/targets/c_headers_2.json
+++ b/Tests/RunCMake/FileAPI/codemodel-v2-data/targets/c_headers_2.json
@@ -10,7 +10,7 @@
       "name": "HEADERS",
       "type": "HEADERS",
       "visibility": "INTERFACE",
-      "baseDirectories": [".*/Tests/RunCMake/FileAPI/fileset$"]
+      "baseDirectories": ["^fileset$"]
     }
   ],
   "sources": [