In short, yes, for example you can run IIS and SQLServer on the same machine.
The long answers requires some more details.
Websites run on port 80, so IIS uses that already. Your application will need to use an unused port, somewhere high above 20k is always good, but there is a list on wikipedia with registered ports: http://en.wikipedia.org/wiki/List_of_TCP_and_UDP_port_numbers
If you pick an unused port, and set the firewall correctly you can host as many applications on the same machine as you like, provided you have enough RAM and whatnot.
If you want to have both run port 80, then you can use IIS to make a webapplication, with a certain subdomain, and redirect that to an ASP.NET application (but that is probably not what you would want to do, if it is, let me know and I could explain more on that)
Hope this helped you on your way :-)