2 Answers

Another kind of ear pain from flying is called aerotitus You can do some stuff to help it if your doctor says it is OK. Avoid flying if you have an ear infection, congestion, allergies or a stuffed up head.  If you can't avoid it, you can take some steps to make your flight more comfortable and maybe avoid aerotitus ear pain.  Take a decongestant every 6 hours for 24 hours before and after your flight.  This will shrink the swollen membranes in your sinus and ear canal.  You can use a pediatric nasal decongestant spray  immediately before you board the plane to shrink the nasal membranes and clear the sinus.  Chewing gum during the entire flight, not just on take off and landing, will open up the Eustachian tubes and keep them open.  There are also ear plugs available that decrease ear pain during flight.  About half an hour before landing you can start to use the pediatric decongestant nasal spray every 5 minutes to keep nasal passages open. 

Source:    http://www.essortment.com/ear-pain-flying-44277.html                                                                                               

i used to get this and its very uncomfortable,went to the doc`s and he said that it is the change in air pressure and the build up of ear wax. had my ears cleared of wax and cleared the problem.

first step is to get you ears checked at the docs.