diff --git a/platform/vcs-impl/src/com/intellij/openapi/vcs/roots/VcsRootDetectorImpl.java b/platform/vcs-impl/src/com/intellij/openapi/vcs/roots/VcsRootDetectorImpl.java
index 9980b3bc7fe1..b38065c0ae73 100644
--- a/platform/vcs-impl/src/com/intellij/openapi/vcs/roots/VcsRootDetectorImpl.java
+++ b/platform/vcs-impl/src/com/intellij/openapi/vcs/roots/VcsRootDetectorImpl.java
@@ -77,7 +77,7 @@ final class VcsRootDetectorImpl implements VcsRootDetector {
 
     detectedRoots.addAll(scanForRootsInsideDir(myProject, dirToScan, null, scannedDirs));
     detectedRoots.addAll(scanForRootsAboveDirs(Collections.singletonList(dirToScan), scannedDirs, detectedRoots));
-    return detectedRoots;
+    return deduplicate(detectedRoots);
   }
 
   private @NotNull Collection<VcsRoot> scanForRootsInContentRoots() {
@@ -106,7 +106,43 @@ final class VcsRootDetectorImpl implements VcsRootDetector {
     detectedAndKnownRoots.addAll(Arrays.asList(ProjectLevelVcsManager.getInstance(myProject).getAllVcsRoots()));
     detectedRoots.addAll(scanDependentRoots(scannedDirs, detectedAndKnownRoots));
 
-    return detectedRoots;
+    return deduplicate(detectedRoots);
+  }
+
+  /**
+   * @return a deduplicated set of {@code detectedRoots} with removed links pointing to the same canonical file.
+   */
+  private static @NotNull Set<VcsRoot> deduplicate(@NotNull Set<VcsRoot> detectedRoots) {
+    if (detectedRoots.size() <= 1) return detectedRoots;
+
+    Set<VcsRoot> result = new HashSet<>();
+
+    Set<VirtualFile> processedCanonicalRoots = new HashSet<>();
+    Set<VcsRoot> rootsUnderSymlink = new HashSet<>();
+    for (VcsRoot root : detectedRoots) {
+      VirtualFile path = root.getPath();
+      VirtualFile canonicalPath = path.getCanonicalFile();
+      if (canonicalPath != null && !path.equals(canonicalPath)) {
+        rootsUnderSymlink.add(root);
+      } else {
+        processedCanonicalRoots.add(path);
+        result.add(root);
+      }
+    }
+
+    if (rootsUnderSymlink.isEmpty()) return detectedRoots;
+
+    for (VcsRoot root : ContainerUtil.sorted(rootsUnderSymlink, Comparator.comparing(root -> root.getPath().toNioPath()))) {
+      VirtualFile canonicalFile = root.getPath().getCanonicalFile();
+      if (processedCanonicalRoots.contains(canonicalFile)) {
+        LOG.debug("Skipping duplicate VCS root %s: root for canonical file '%s' is already detected".formatted(root, canonicalFile));
+      } else {
+        processedCanonicalRoots.add(canonicalFile);
+        result.add(root);
+      }
+    }
+
+    return result;
   }
 
   private @NotNull Set<VcsRoot> scanForRootsInsideDir(@NotNull Project project,
diff --git a/platform/vcs-tests/testSrc/com/intellij/openapi/vcs/roots/VcsRootDetectorTest.kt b/platform/vcs-tests/testSrc/com/intellij/openapi/vcs/roots/VcsRootDetectorTest.kt
index b93158d0502b..80fa91494cab 100644
--- a/platform/vcs-tests/testSrc/com/intellij/openapi/vcs/roots/VcsRootDetectorTest.kt
+++ b/platform/vcs-tests/testSrc/com/intellij/openapi/vcs/roots/VcsRootDetectorTest.kt
@@ -1,4 +1,4 @@
-// Copyright 2000-2020 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license that can be found in the LICENSE file.
+// Copyright 2000-2025 JetBrains s.r.o. and contributors. Use of this source code is governed by the Apache 2.0 license.
 package com.intellij.openapi.vcs.roots
 
 import com.intellij.openapi.components.service
@@ -8,8 +8,11 @@ import com.intellij.openapi.vcs.VcsTestUtil.assertEqualCollections
 import com.intellij.openapi.vfs.VirtualFile
 import com.intellij.testFramework.PsiTestUtil
 import com.intellij.testFramework.VfsTestUtil
+import com.intellij.testFramework.utils.io.createDirectory
+import com.intellij.testFramework.utils.io.createFile
 import org.jetbrains.jps.model.serialization.PathMacroUtil
 import java.util.Collections.emptyList
+import kotlin.io.path.createSymbolicLinkPointingTo
 
 class VcsRootDetectorTest : VcsRootBaseTest() {
   fun `test no roots`() {
@@ -164,6 +167,95 @@ class VcsRootDetectorTest : VcsRootBaseTest() {
     expect(projectRoot)
   }
 
+  // IJPL-172487
+  fun `test root referenced via child symlink should not be duplicated`() {
+    initRepository(projectRoot)
+
+    // Created layout:
+    // project/
+    // -child/
+    // --test
+    // --root-symlink -> project
+    val targetDir = projectNioRoot.createDirectory("child")
+    targetDir.createFile("test")
+    targetDir.resolve("root-symlink").createSymbolicLinkPointingTo(projectNioRoot)
+
+    VfsTestUtil.syncRefresh()
+
+    PsiTestUtil.addContentRoot(rootModule, projectRoot)
+
+    expect(projectRoot)
+  }
+
+  // IJPL-181017
+  fun `test root has symlink parent`() {
+    val symlink = projectNioRoot.resolve("symlink")
+    val projectSibling = testNioRoot.createDirectory("project-sibling")
+    symlink.createSymbolicLinkPointingTo(projectSibling)
+    VfsTestUtil.syncRefresh()
+
+    val vcsRoot = createVcsRoots("symlink/repo-root")
+    // Expected `project/symlink/repo-root` which is not a canonical path `project-sibling/repo-root`
+    expect(vcsRoot)
+  }
+
+
+  fun `test multiple roots under symlink`() {
+    val symlink = projectNioRoot.resolve("symlink")
+    val projectSibling = testNioRoot.createDirectory("project-sibling")
+    symlink.createSymbolicLinkPointingTo(projectSibling)
+    VfsTestUtil.syncRefresh()
+
+    // Created layout:
+    // project/
+    // -symlink -> project-sibling
+    // project-sibling/
+    // -root1
+    // -root2
+    // -root3
+    val roots = createVcsRoots("symlink/root1", "symlink/root2", "symlink/root3")
+    expect(roots)
+  }
+
+  fun `test multiple roots with symlink target outside project`() {
+    initRepository(projectRoot)
+
+    val symlink = projectNioRoot.resolve("symlink")
+    val projectSibling = testNioRoot.createDirectory("project-sibling")
+    symlink.createSymbolicLinkPointingTo(projectSibling)
+    VfsTestUtil.syncRefresh()
+
+    val vcsRoot = createVcsRoots("symlink/repo-root")
+    expect(vcsRoot + projectRoot)
+  }
+
+  // Combined scenario for IJPL-172487 and IJPL-181017
+  fun `test symlinks under symlinks`() {
+    val symlink = projectNioRoot.resolve("symlink")
+    val projectSibling = testNioRoot.createDirectory("project-sibling")
+    symlink.createSymbolicLinkPointingTo(projectSibling)
+    VfsTestUtil.syncRefresh()
+
+    val vcsRoot = createVcsRoots("symlink/repo-root")
+
+    // Created layout:
+    // project/
+    // -symlink -> project-sibling/
+    // project-sibling/
+    // -repo-root
+    // --test
+    // --sublink -> repo-root
+    val repoRoot = symlink.resolve("repo-root")
+    repoRoot.createFile("test")
+    val linkToRepo = repoRoot.resolve("sublink")
+    linkToRepo.createSymbolicLinkPointingTo(repoRoot)
+
+    VfsTestUtil.syncRefresh()
+
+    // Expected only `project/symlink/repo-root`
+    expect(vcsRoot)
+  }
+
   private fun createVcsRoots(vararg relativePaths: String, registerContentRoot: Boolean = true): List<VirtualFile> {
     return createVcsRoots(listOf(*relativePaths), registerContentRoot)
   }