Ti riporto l'esempio di MSDN:

codice:
<html>
  <head>
    <script language="C#" runat="server">
      public void Page_Load(Object sender, EventArgs e)
      {

        if (!this.IsStartupScriptRegistered("Startup"))
        {
          // Form the script to be registered at client side.
          String scriptString = "<script language=JavaScript> function DoClick() {";
          scriptString += "showMessage2.innerHTML='<h4>Welcome to Microsoft .NET!</h4>'}";
          scriptString += "function Page_Load(){ showMessage1.innerHTML=";
          scriptString += "'<h4>RegisterStartupScript Example</h4>'}<";
          scriptString += "/";
          scriptString += "script>";
          this.RegisterStartupScript("Startup", scriptString);
        }
      }
     </script>
  </head>
  <body topmargin="20" leftmargin="10" onload="Page_Load()">
	 <form id="myForm" runat="server">
		<span id="showMessage1"></span>
		

		<input type="button" value="ClickMe" onclick="DoClick()">
		

		<span id="showMessage2"></span>
	 </form>
  </body>
</html>