Francis Tregian was the son of Francis Tregian the Elder and Mary Stourton. He is thought to have been born in 1574. (The birth year is derived from a household list drawn up in 1594 at the death of his teacher William Allen which referred to Tregian as being 20 years old: "molto nobile, di 20 anni, se colare di ingennio delicessimo dotto in filosofia, in musica et nella lingua latina." Not only is this the only document suggesting his age but it is also the only document associating him with music.) In 1577 his father was arrested for being a Roman Catholic and sheltering priests. He was imprisoned and dispossessed, and the Tregian family had to leave their manor house in Probus, Cornwall.