diff --git a/src/waypoint_cmd.cpp b/src/waypoint_cmd.cpp
--- a/src/waypoint_cmd.cpp
+++ b/src/waypoint_cmd.cpp
@@ -20,6 +20,7 @@
 #include "pathfinder/yapf/yapf_cache.h"
 #include "strings_func.h"
 #include "viewport_func.h"
+#include "viewport_kdtree.h"
 #include "window_func.h"
 #include "date_func.h"
 #include "vehicle_func.h"
@@ -225,11 +226,15 @@ CommandCost CmdBuildRailWaypoint(TileInd
 	}
 
 	if (flags & DC_EXEC) {
+		bool need_sign_update = false;
 		if (wp == NULL) {
 			wp = new Waypoint(start_tile);
+			need_sign_update = true;
 		} else if (!wp->IsInUse()) {
 			/* Move existing (recently deleted) waypoint to the new location */
+			_viewport_sign_kdtree.Remove(ViewportSignKdtreeItem::MakeWaypoint(wp->index));
 			wp->xy = start_tile;
+			need_sign_update = true;
 		}
 		wp->owner = GetTileOwner(start_tile);
 
@@ -244,6 +249,7 @@ CommandCost CmdBuildRailWaypoint(TileInd
 		if (wp->town == NULL) MakeDefaultName(wp);
 
 		wp->UpdateVirtCoord();
+		if (need_sign_update) _viewport_sign_kdtree.Insert(ViewportSignKdtreeItem::MakeWaypoint(wp->index));
 
 		const StationSpec *spec = StationClass::Get(spec_class)->GetSpec(spec_index);
 		byte *layout_ptr = AllocaM(byte, count);
@@ -310,6 +316,7 @@ CommandCost CmdBuildBuoy(TileIndex tile,
 			wp = new Waypoint(tile);
 		} else {
 			/* Move existing (recently deleted) buoy to the new location */
+			_viewport_sign_kdtree.Remove(ViewportSignKdtreeItem::MakeWaypoint(wp->index));
 			wp->xy = tile;
 			InvalidateWindowData(WC_WAYPOINT_VIEW, wp->index);
 		}
@@ -328,6 +335,7 @@ CommandCost CmdBuildBuoy(TileIndex tile,
 		MarkTileDirtyByTile(tile);
 
 		wp->UpdateVirtCoord();
+		_viewport_sign_kdtree.Insert(ViewportSignKdtreeItem::MakeWaypoint(wp->index));
 		InvalidateWindowData(WC_WAYPOINT_VIEW, wp->index);
 	}