Posterior ankle pain with kicking is common with a condition called posterior ankle impingement syndrome (PAIS). This problem is also known as ankle block, nutcracker syndrome, or os trigonum syndrome.
Whether or not you wear shoes while kicking may not be as important as the kicking motion itself. PAIS occurs with forced ankle plantar flexion. This refers to a position with the toes pointed down with force or compression. Kicking a football certainly fits the description of the motion that can cause PAIS.
Before putting your shoes back on, you may want to get an X-ray or MRI. There may be a fracture, bone fragment, or soft tissue impingement to account for your symptoms. Once you know the true cause of your problem then you follow your doctor's advice.