It should work. Start with something simple:
<%@ Master Language="C#" AutoEventWireup="true" CodeFile="MasterPage.master.cs" Inherits="MasterPage" %>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<script type="text/javascript" language="javascript">
function MasterPageFunction()
{
alert("MasterPageFunction called");
}
</script>
Child Page:
<input id="Button2" type="button" value="MP function" onclick="MasterPageFunction();"/>