Crossword Dictionary

pain 

pain, hurting - n 
a symptom of some physical hurt or disorder; "the patient developed severe pain and distension" 

wordplays

If you feel pain, you feel acute physical or emotional discomfort. A sprained ankle will pain you. So will news of a loved one's death. If you "take pain" over something, it means you're being careful.

An annoying person can be described as a pain––it's understood that they don't cause you actual physical pain, but cause you emotional discomfort and distress. You can also describe this person as a "pain in the neck," "a pain in the butt," or "a royal pain."

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etymology

late 13c., peine, "the agony suffered by Christ;" c. 1300, "punishment," especially for a crime, "legal punishment of any sort" (including fines and monetary penalties); also "condition one feels when hurt, opposite of pleasure," including mental or emotional suffering, grief, distress; from Old French peine "difficulty, woe, suffering, punishment, Hell's torments" (11c.), from Latin poena "punishment, penalty, retribution, indemnification" (in Late Latin also "torment, hardship, suffering"), from Greek poinÄ“ "retribution, penalty, quit-money for spilled blood," from PIE *kwei- "to pay, atone, compensate" (see penal).

etymonline.com