diff --git a/src/cdk/overlay/position/flexible-connected-position-strategy.spec.ts b/src/cdk/overlay/position/flexible-connected-position-strategy.spec.ts
index 8d517776d2f5..b65b44bb9094 100644
--- a/src/cdk/overlay/position/flexible-connected-position-strategy.spec.ts
+++ b/src/cdk/overlay/position/flexible-connected-position-strategy.spec.ts
@@ -1361,6 +1361,33 @@ describe('FlexibleConnectedPositionStrategy', () => {
       expect(boundingBox.style.right).toBe('0px');
     });
 
+    it('should calculate the bottom offset correctly with a viewport margin', () => {
+      const viewportMargin = 5;
+
+      originElement.style.top = `${OVERLAY_HEIGHT / 2}px`;
+      originElement.style.right = '200px';
+
+      positionStrategy
+        .withFlexibleHeight()
+        .withViewportMargin(viewportMargin)
+        .withPositions([
+          {
+            originX: 'start',
+            originY: 'top',
+            overlayX: 'start',
+            overlayY: 'bottom'
+          }
+        ]);
+
+      attachOverlay({positionStrategy});
+
+      const originRect = originElement.getBoundingClientRect();
+      const overlayRect = overlayRef.overlayElement.getBoundingClientRect();
+
+      expect(Math.floor(overlayRect.bottom)).toBe(Math.floor(originRect.top));
+      expect(Math.floor(overlayRect.top)).toBe(viewportMargin);
+    });
+
   });
 
   describe('onPositionChange with scrollable view properties', () => {
diff --git a/src/cdk/overlay/position/flexible-connected-position-strategy.ts b/src/cdk/overlay/position/flexible-connected-position-strategy.ts
index 4792318a89d4..0ad1375488f0 100644
--- a/src/cdk/overlay/position/flexible-connected-position-strategy.ts
+++ b/src/cdk/overlay/position/flexible-connected-position-strategy.ts
@@ -580,6 +580,7 @@ export class FlexibleConnectedPositionStrategy implements PositionStrategy {
    */
   private _calculateBoundingBoxRect(origin: Point, position: ConnectedPosition): BoundingBoxRect {
     const viewport = this._viewportRect;
+    const isRtl = this._isRtl();
     let height, top, bottom;
 
     if (position.overlayY === 'top') {
@@ -587,9 +588,11 @@ export class FlexibleConnectedPositionStrategy implements PositionStrategy {
       top = origin.y;
       height = viewport.bottom - origin.y;
     } else if (position.overlayY === 'bottom') {
-      // Overlay is opening "upward" and thus is bound by the top viewport edge.
-      bottom = viewport.height - origin.y + this._viewportMargin;
-      height = viewport.height - bottom;
+      // Overlay is opening "upward" and thus is bound by the top viewport edge. We need to add
+      // the viewport margin back in, because the viewport rect is narrowed down to remove the
+      // margin, whereas the `origin` position is calculated based on its `ClientRect`.
+      bottom = viewport.height - origin.y + this._viewportMargin * 2;
+      height = viewport.height - bottom + this._viewportMargin;
     } else {
       // If neither top nor bottom, it means that the overlay
       // is vertically centered on the origin point.
@@ -607,13 +610,13 @@ export class FlexibleConnectedPositionStrategy implements PositionStrategy {
 
     // The overlay is opening 'right-ward' (the content flows to the right).
     const isBoundedByRightViewportEdge =
-        (position.overlayX === 'start' && !this._isRtl()) ||
-        (position.overlayX === 'end' && this._isRtl());
+        (position.overlayX === 'start' && !isRtl) ||
+        (position.overlayX === 'end' && isRtl);
 
     // The overlay is opening 'left-ward' (the content flows to the left).
     const isBoundedByLeftViewportEdge =
-        (position.overlayX === 'end' && !this._isRtl()) ||
-        (position.overlayX === 'start' && this._isRtl());
+        (position.overlayX === 'end' && !isRtl) ||
+        (position.overlayX === 'start' && isRtl);
 
     let width, left, right;
 
@@ -886,7 +889,7 @@ export class FlexibleConnectedPositionStrategy implements PositionStrategy {
     return {
       top:    scrollPosition.top + this._viewportMargin,
       left:   scrollPosition.left + this._viewportMargin,
-      right:  scrollPosition.left + width  - this._viewportMargin,
+      right:  scrollPosition.left + width - this._viewportMargin,
       bottom: scrollPosition.top + height - this._viewportMargin,
       width:  width  - (2 * this._viewportMargin),
       height: height - (2 * this._viewportMargin),