Kerll was the son of Caspar Kerll and Catharina Hendel (married 1626). He was born in 1627 in Adorf, where his father served as organist of the Michaeliskirche (appointed after building the church organ with Jacob Schädlich). Caspar Kerll probably gave music lessons to his son, who apparently demonstrated exceptional musical abilities; by 1641 he was already composing and sometime later during the early 1640s he was sent to Vienna to study under Giovanni Valentini, court Kapellmeister and composer. Kerll's professional career started in Vienna, where he served as organist, and continued in approximately 1647/8, when Archduke Leopold Wilhelm of Austria (then the governor of the Spanish Netherlands) employed him as chamber organist for the new residential palace in Brussels.