You need to add runat = server and use onserverclick for Input type Button
HTML
<div>
<input id="checkbox1" runat="server" type="checkbox" name="name" value="" />
<input type="button" runat="server" onserverclick="ValidateCheckBox" name="name" value="Validate" />
</div>
C#
protected void ValidateCheckBox(object sender, EventArgs e)
{
if (this.checkbox1.Checked != true)
{
ClientScript.RegisterStartupScript(this.GetType(), "alert", "alert('Please Check the CheckBox')", true);
}
}