What you describe is not uncommon, particularly as we spend increasing amounts of time reading, staring at a computer or TV screen, driving or engaging in other activities that require us to focus and concentrate for prolonged periods.
Our eyes contain various muscles responsible for changing the diameter of our pupil, changing the curvature of the lens and the movements of the eye itself. Like any muscle, prolonged use can lead to fatigue. Tired muscles require greater effort to function effectively, and being tired to begin with can make matters worse.
What most people refer to as eyestrain can cause headaches, nausea and general lethargy, as well as make the eyeballs themselves hurt. So, as with any other workout, it is recommended that you take regular rest breaks for your eyes - say, every one to two hours. Look away from what you are doing. Practice relaxation exercises for your eyes, face, neck and shoulders. Go for a quick walk, even if it is only to grab a drink or snack, or head outside for some fresh air.
I also recommend that you see an OPTHAMOLOGIST. They can test your eyes and let you know whether or not you need glasses for close work (reading glasses) or if there is a change in your current prescription. They also can diagnose and treat eye disorders. Corrective lenses can assist you in focusing, so that your eyes aren't working so hard. They may just recommend exercises for your eye muscles to help them function more effectively. Also, they can treat medical disorders. Their testing is usually more through than an Optician or Optometrist. Once your condition is diagnosed or treated, follow up may be done by an Optician or Optometrist if you have no medical need of an M.D.