One of the most common issues we see in clinic is neck and shoulder pain caused by upper quadrant dysfunction. The classic protracted (rounded) shoulders and chin poke posture, accentuated by a weak posterior chain- muscles in the back. I amazed at the amount of athletes I see who adopt this position naturally, and I see it a lot in people who spend their days behind a desk! Sound familiar?
There are many issues. Scapula positioning is off which is unlikely to cause problems on its own, but over time can lead to the weakening of the structures which control the scapula and this can bring problems when more dynamic movement is needed.
Another issue is the neck posture, increased loading of the posterior portion of the disks and vertebrae in the cervical spine will likely lead to increased rates of degeneration and can easily lead into painful disorders like radiculopathy or thoracic outlet syndrome- where nerves get trapped and can give terrible pain down into the shoulders and arms.
The solution is simple, posterior chain strengthening- strengthening the muscles of the scapula in the correct way, and postural awareness. My go-to task for clients is to set up a visual prompt on their desk at work, which reminds them to correct posture. This helps to turn bad habits into good habits and posture improves with it. It's much easier to fall into bad habits than good, but with regular mental cues, you can turn posture into a good habit and after a while you'll keep a good posture autonomously.
Good posture is perhaps a bit too general however, and evidence finds that sitting in any position, no matter how much it represents what we state to be 'good posture', will end up causing problems. Humans were not designed to sit behind a desk all day, and so the best thing you can do is get up from behind your desk at regular intervals, stretch, activate some muscle. Good balance within the muscle groups cannot be brought about by sitting behind a desk, because we only use muscles groups in the anterior chain- in the front of the body. This is where the problem begins.
So in summary, prevention is better than cure. If you can get up, please do. If you can't then you need to do something before or after work that counteracts everything whilst behind your desk. Spend 30 minutes out of the 1440 minutes we have each day doing some exercise, and these issues will likely never arise in the first place