Visualforce page that calls another Visualforce page upon confirming from javascript.

Visualforce Page:

<apex:page standardController="Account">
    <apex:form>
        <apex:pageBlock>
            <apex:commandButton value="Open VF Page" onclick="OpenVFPage()"/>
        </apex:pageBlock>
    
    <script>
      function OpenVFPage(){
        var isConfirm = confirm('Do you want to open a new Visualforce Page?');
        if(isConfirm)
           window.open('/apex/YourVisualForcePage');
      }
     </script>
    </apex:form>
</apex:page>

Similarly, if you want to open a visualforce page from a custom button using javascript then use following piece of code.

{!REQUIRESCRIPT("/soap/ajax/22.0/connection.js")} 
var isConfirm = confirm('Do you want to open new Visualforce Page?');
if(isConfirm){
	window.parent.location.href="/apex/YourVisualforcePage";
}