As far as I know there is no fixed rule for words ending with cia - many are not accented - not just farmacia: others include ambulancia, abundancia, ciencia, constancia, conciencia, denuncia, ganancia, justicia, creencia, inercia, Francia, resonancia, estancia, ganancia, urgencia.
If there is a general rule that names for establishments like barber?a, cafeter?a, ferreter?a, mercer?a, papeler?a, etc. should have that final stress, note they all have ria at the end, unlike farmacia.
My sister, a Spanish teacher, mentioned that this is a mistake she often has to correct, students pronouncing it "farmac?a".