Jan Linsen was born in Hoorn around 1602 or 1603. An anonymous drawing from around 1623 shows Linsen together with other founding members of the 'Bentvueghels' and tells us his nickname, 'Hermafrodito'. Thus his presence in Rome is documented; however, the length of his stay has not been established. In the archives of the Parochie Sancti Nicolai in Rome, he is listed in 1625 as living in the Strada dell'Olmo, from which he moved in the following year. A drawing of his with a Roman motif dated 1630 (Amsterdam, Rijksprentenkabinet) suggests that at that point he was still residing in the Eternal City. Sylistic parallels with the work of Bartholomeus Breenbergh suggest contact between the two painters, who were living in Rome at the same time and had possibly known each other since they were children in Hoorn. Dated paintings indicate that Linsen began to take up mythological subjects before Breenbergh did.
According to Houbraken, after boarding a ship in Italy, Linsen was kidnapped by 'Moors' and then abandoned. Supposedly he later depicted the leader of the 'Moors' in a painting, as Houbraken relates in reference to a letter from 1718. Jan Linsen died in 1635 after an altercation in a tavern in Hoorn.