diff --git a/bundles/org.eclipse.ui.ide/src/org/eclipse/ui/ide/dialogs/ResourceTreeAndListGroup.java b/bundles/org.eclipse.ui.ide/src/org/eclipse/ui/ide/dialogs/ResourceTreeAndListGroup.java
index 8a6fae213b8..74adfe8495d 100644
--- a/bundles/org.eclipse.ui.ide/src/org/eclipse/ui/ide/dialogs/ResourceTreeAndListGroup.java
+++ b/bundles/org.eclipse.ui.ide/src/org/eclipse/ui/ide/dialogs/ResourceTreeAndListGroup.java
@@ -23,6 +23,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.Objects;
 import java.util.Set;
 
 import org.eclipse.core.commands.common.EventManager;
@@ -73,6 +74,15 @@ public void checkStateChanged(final CheckStateChangedEvent event) {
 			BusyIndicator.showWhile(treeViewer.getControl().getDisplay(),
 					() -> {
 						if (event.getCheckable().equals(treeViewer)) {
+							/*
+							 * On Windows, checking an item does not automatically update the tree selection
+							 * like on Linux environment. Force the checked element to become the current
+							 * selection so SelectionListener and CheckListener stay in sync together
+							 */
+							Object currentSelection = treeViewer.getStructuredSelection().getFirstElement();
+							if (!Objects.equals(currentSelection, event.getElement())) {
+								treeViewer.setSelection(new StructuredSelection(event.getElement()), true);
+							}
 							treeItemChecked(event.getElement(), event
 									.getChecked());
 						} else {