I am an eye doctor and I can tell you many, many people have similar symptoms from prolonged computer use. This is due to a number of reasons. The flicker rate of the screen does cause fatigue like Gabby said. We blink less when staring a computer screen, so your eyes dry out.
Also, it is difficult for the eyes to focus on a computer screen because the edges of the letters are not as crisp as printed material (this is much better than it used to be, remember the black screen with green block letters!?)
Here are some simple ways to reduce eyestrain when working on the computer:
Every twenty minutes take a break for at least 20 seconds and look at something at least 20 feet away. This lets the muscles in your eye responsible for focusing completely relax and recover, thus letting you work longer without eyestrain.
Keep a bottle of artificial tear drops next to your computer (but not a “get the red out” drop, just artificial tears for lubrication). Put a drop in each eye about once an hour.
Remember, your blink rate goes down when concetrating or reading, this will help the eyes stay more moist. The drops work best if used BEFORE your eyes feel dry/ irritated/ bloodshot, etc. Think of it like being thirsty – better to prevent thirst to stay hydrated than try to “catch up” once you are thirsty.
Reduce glare on the screen to make it easier for your eyes to focus. This includes reflections off the screen from windows or lighting. If possible, have your printed material illuminated with as direct of a light as possible.
For example, a flexible lamp. This way you can shine the light where you need it and keep it off your computer screen. Some folks even find it easier on the eyes to wear dark colored shirts – light colored shirts reflect off the screen and cause a little bit of glare. Reducing causes of glare will make it easier for your eyes to focus and reduce eyestrain.
Finally (and maybe this should be first), make sure that your glasses or contact lens prescription is up to date and accurate. I often prescribe “computer glasses” to let the eyes be more relaxed (not work so hard focusing, etc) when working on the computer.
A computer prescription is slightly different than a reading presciption, any eye doc should know how to determine the ideal power for computer glasses based on your eye exam findings.
If you are age 40-50, have never needed glasses, but are having trouble with the computer – you may be noticing normal changes that come at this age and it may be time for some computer glasses or reading glasses. In other words, time to get your eyes checked.
Sorry for the long reply, but there is your free professional advice.