Your chair is too high.
If your chair is high enough that your feet are dangling, you may experience foot or knee pain. Make sure you use a footrest to support your feet. See Chair Setup and Usage.
You've been sitting too long without a break.
Circling your ankles a bit may help improve circulation and make your feet feel better. See Stretches and Exercises.
Your CPU is placed under your desk, forcing your feet into an uncomfortable position.
Placing your CPU under the desk where your legs normally go leaves less room for your feet and ankles. This can lead to cramped space and pain in your feet if you can't move them freely - or if you have to adjust your sitting position around the CPU. You may want to consider a CPU holder. See Desk Overview and Accessories or Desk Setup and Usage.
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