diff --git a/src/compiler/moduleSpecifiers.ts b/src/compiler/moduleSpecifiers.ts
index 1850220a411c1..aed224318da80 100644
--- a/src/compiler/moduleSpecifiers.ts
+++ b/src/compiler/moduleSpecifiers.ts
@@ -321,7 +321,9 @@ namespace ts.moduleSpecifiers {
         // Get a path that's relative to node_modules or the importing file's path
         // if node_modules folder is in this folder or any of its parent folders, no need to keep it.
         const pathToTopLevelNodeModules = getCanonicalFileName(moduleSpecifier.substring(0, parts.topLevelNodeModulesIndex));
-        if (!(startsWith(sourceDirectory, pathToTopLevelNodeModules) || globalTypingsCacheLocation && startsWith(getCanonicalFileName(globalTypingsCacheLocation), pathToTopLevelNodeModules))) {
+        // If PnP is enabled the node_modules entries we'll get will always be relevant even if they
+        // are located in a weird path apparently outside of the source directory
+        if (!process.versions.pnp && !(startsWith(sourceDirectory, pathToTopLevelNodeModules) || globalTypingsCacheLocation && startsWith(getCanonicalFileName(globalTypingsCacheLocation), pathToTopLevelNodeModules))) {
             return undefined;
         }