The son of painter Frans Francken I, Frans II presumably served as an apprentice in the studio of his father, and it is also likely that he trained in Paris with his uncle Hieronymus I, perhaps at the same time as his brother, Hieronymus II. In 1605 he became a master in the Antwerp Guild of St. Luke, and served as its deacon in 1616.
Though a contemporary of Rubens, Francken painted in a style more influenced by Venetian Mannerism and the small scale narrative scenes of Hendrik van Balen I. As was standard practice in this era of Flemish art, Francken often worked in collaboration with other artists. Francken himself specialized in painting small figures, and his best works were often produced in collaboration with painters who specialized in landscape and architecture. The Crucifixion, ca. 1600-1610, bears the stamp of the Antwerp Guild and mark of Michel Vriendt. It was painted by Francken possibly in conjunction with other artists. Francken is known to have collaborated with Andries Daniels, Abraham Govaerts, Abel Grimmer, Alexander Keirincx, Joos de Momper, Jan Wildens and Gerard Seghers.