How far are you commuting one way? Ideally you wouldn't arrive and then immediately sit down; give yourself a 10 to 15 minute cool down period with some walking and stretching if possible.
The stiffness could be coming from other factors, like the ergonomics or lack thereof of your workstation. See if you can have a variable height monitor and keyboard, so that you can work standing up part of the day and seated the rest of the day.