In 1602, Overall was made rector of Algarkirk, Lincoln; he held the living for three years. With the support of Sir Fulke Greville he was nominated Dean of St Paul's Cathedral in London. On 6 June, Lawrence Barker, vicar of St Botolph Aldersgate, and a former colleague at Trinity, spoke at Paul's Cross of the "gravity & learning and life" of the new dean. The Deanery itself became a haven for scholars like Scultetus who shared the house with him. Overall himself, according to the radical preacher Thomas Scott, emerged as something of an Anglo-Catholic. Overall was also granted the Prebendary of Tottenhall.