Use a
PostBackTrigger
<asp:ScriptManager ID="scriptManager" runat="server">
<asp:UpdatePanel ID="updatePanel" runat="server">
<ContentTemplate>
<asp:Button ID="btnSubmit" runat="server" OnClientClick="javascript:alert(1);" Text="Click"
onclick="btnSubmit_Click" />
</ContentTemplate>
<Triggers>
<asp:PostBackTrigger ControlID="btnSubmit" />
</Triggers>
</asp:UpdatePanel>