diff --git a/src/cdk/collections/selection-model.ts b/src/cdk/collections/selection-model.ts
index c5ac4daff494..fa295aea5b49 100644
--- a/src/cdk/collections/selection-model.ts
+++ b/src/cdk/collections/selection-model.ts
@@ -208,11 +208,16 @@ export class SelectionModel<T> {
 
   /** Deselects a value. */
   private _unmarkSelected(value: T) {
+    let comparableValue: T | null = null;
     if (this.isSelected(value)) {
-      this._selection.delete(value);
-
+      if (this.compareWith) {
+        comparableValue = this._getComparableValue(value) as T;
+        this._selection.delete(comparableValue);
+      } else {
+        this._selection.delete(value);
+      }
       if (this._emitChanges) {
-        this._deselectedToEmit.push(value);
+        this._deselectedToEmit.push(comparableValue || value);
       }
     }
   }
@@ -238,6 +243,19 @@ export class SelectionModel<T> {
   private _hasQueuedChanges() {
     return !!(this._deselectedToEmit.length || this._selectedToEmit.length);
   }
+
+  /** Returns a value that is comparable to inputValue by applying compareWith function, returns null if none.*/
+  private _getComparableValue(inputValue: T): T | null {
+    let comparableValue: T | null = null;
+    if (this.compareWith) {
+      this._selection.forEach(selectedValue => {
+        if (this.compareWith?.call(undefined, inputValue, selectedValue)) {
+          comparableValue = selectedValue;
+        }
+      });
+    }
+    return comparableValue;
+  }
 }
 
 /**
diff --git a/src/cdk/collections/selection.spec.ts b/src/cdk/collections/selection.spec.ts
index ac430f962f23..3242865ff8ef 100644
--- a/src/cdk/collections/selection.spec.ts
+++ b/src/cdk/collections/selection.spec.ts
@@ -279,4 +279,24 @@ describe('SelectionModel', () => {
     let singleSelectionModel = new SelectionModel();
     expect(singleSelectionModel.isMultipleSelection()).toBe(false);
   });
+
+  it('should deselect value if comparable to another one', () => {
+    type T = {key: number; value: string};
+    const v1: T = {key: 1, value: 'blue'};
+    const v2: T = {key: 1, value: 'green'};
+    const compareFun = (x: T, y: T) => x.key === y.key;
+    const model = new SelectionModel<T>(false, [v1], false, compareFun);
+    model.deselect(v2);
+    expect(model.selected.length).toBe(0);
+  });
+
+  it('should not deselect value if not comparable to another one', () => {
+    type T = {key: number; value: string};
+    const v1: T = {key: 1, value: 'blue'};
+    const v2: T = {key: 2, value: 'apple'};
+    const compareFun = (x: T, y: T) => x.key === y.key;
+    const model = new SelectionModel<T>(false, [v1], false, compareFun);
+    model.deselect(v2);
+    expect(model.selected.length).toBe(1);
+  });
 });