You need to use ScriptManager.RegisterStartupScript for Ajax.
protected void ButtonPP_Click(object sender, EventArgs e) { if (radioBtnACO.SelectedIndex < 0) { string csname1 = "PopupScript"; var cstext1 = new StringBuilder(); cstext1.Append("alert('Please Select Criteria!')"); ScriptManager.RegisterStartupScript(this, GetType(), csname1, cstext1.ToString(), true); } }