diff --git a/packages/pyright-internal/src/analyzer/program.ts b/packages/pyright-internal/src/analyzer/program.ts
index 9084964d1..6dd178d73 100644
--- a/packages/pyright-internal/src/analyzer/program.ts
+++ b/packages/pyright-internal/src/analyzer/program.ts
@@ -293,9 +293,7 @@ export class Program {
         }
 
         // Add the new files. Only the new items will be added.
-        // Normalize paths to ensure consistency with other code paths.
-        const normalizedFilePaths = filePaths.map(path => normalizePathCase(this._fs, path));
-        this.addTrackedFiles(normalizedFilePaths);
+        this.addTrackedFiles(filePaths);
 
         return this._removeUnneededFiles();
     }
diff --git a/packages/pyright-scip/src/indexer.ts b/packages/pyright-scip/src/indexer.ts
index db6840a3f..65272f657 100644
--- a/packages/pyright-scip/src/indexer.ts
+++ b/packages/pyright-scip/src/indexer.ts
@@ -9,6 +9,7 @@ import { createFromRealFileSystem } from 'pyright-internal/common/realFileSystem
 import { ConfigOptions } from 'pyright-internal/common/configOptions';
 import { TreeVisitor } from './treeVisitor';
 import { FullAccessHost } from 'pyright-internal/common/fullAccessHost';
+import { normalizePathCase } from 'pyright-internal/common/pathUtils';
 import * as url from 'url';
 import { ScipConfig } from './lib';
 import { SourceFile } from 'pyright-internal/analyzer/sourceFile';
@@ -122,7 +123,9 @@ export class Indexer {
         this.importResolver = new ImportResolver(fs, this.pyrightConfig, host);
 
         this.program = new Program(this.importResolver, this.pyrightConfig);
-        this.program.setTrackedFiles([...this.projectFiles]);
+        // Normalize paths to ensure consistency with other code paths.
+        const normalizedProjectFiles = [...this.projectFiles].map((path: string) => normalizePathCase(fs, path));
+        this.program.setTrackedFiles(normalizedProjectFiles);
 
         if (scipConfig.projectNamespace) {
             setProjectNamespace(scipConfig.projectName, this.scipConfig.projectNamespace!);