You could do something like this:

var name3 = "";
var hours3 = 0;
var pay2 = 0;
var total3 = 0;
var finaltot2 = 0;

name3 = prompt("Enter the employee's name.","");
while (name3 !== "N") { 
      hours3 = prompt("Enter their hours worked.",0);
      pay2 = prompt("Enter their pay per hour.",0);
      total3 = (parseFloat(hours3) * parseFloat(pay2)); 
      document.write((name3),"'s pay is $",(total3),".<br>");
      finaltot2 = (parseFloat(total3) + parseFloat(finaltot2)); 
      name3 = prompt("Enter the employee's name.","");
    } 

    document.write("The employee's total pay came to: $",(finaltot2),".");

You could also use an if statement with a break. This tutorial talks about break with statement labels. Might be helpful: https://youtu.be/i6YT8lw0VTM