I’m not a 400 (err.. i5) guy myself but I’ve had some experiences with them. I can speak from a windows perspective and say from my searches on the internet it would be possible.
Here is a link to a discussion that looks promising. From the windows side you are going to want to be sure whatever credentials you use on the i5 has access to do what you want on the windows side. Additionally, from my experiences automating processes on windows you are going to want to be sure that your user you are running as on the windows box has a profile created (has logged on) and depending on what you do may need other rights, like act as part of the operating syste, run as a servcie, etc.
In addition to credentials, you’ll need something installed on the W2K3 box to receive and process the commands that you send to it. The iSeries Access Remote Command service is what is often used (meaning that a basic install of iSeries Access is needed on the W2K3 PC.)
If iSeries Access is not an option for you, then you’ll be looking for any kind of rexec() server that you can find that is available for W2K3. I have a vague memory that a native rexec() server is available with W2K3, but that might be wishful thinking. If not, internet searches can turn up alternatives. The rexec() facility is widely known.
On your AS/400 side, there shouldn’t be anything needed beyond a basic OS and TCP/IP setup. A rexec() server and client are both in the base system. (Server is started with STRTCPSVR *REXEC and configured with CHGRXCA or with iSeries Navigator.)