Probably from an original form *Pärnäoja, from dialectal pärnä + oja. The modern vowel -e- in Finnish would be influence from the Swedish form Pernå, which is from the same Finnish name (with oja translated as å).[1]
The internal locative cases (inessive, illative and elative) are used with this place name when referring to a location; for example, "in Pernaja" is Pernajassa.
^ Sirkka Paikkala, editor (2007), Suomalainen paikannimikirja [Book of Finnish Place names] (in Finnish), Helsinki: Karttakeskus, Kotimaisten kielten tutkimuskeskus, →ISBN