Hooker was likely born in Leicestershire at "Marfield" (Marefield or possibly Markfield) or Birstall. He went to Dixie Grammar School at Market Bosworth. Family genealogist Edward Hooker linked Thomas Hooker to the Hooker family in Devon which produced the theologian and clergyman Richard Hooker. Other Hooker genealogists, however, have traced Thomas Hooker to Leicestershire. Positive evidence linking Thomas to Leicestershire is lacking since the Marefield parish records from before 1610 perished. Any link to the Rev. Richard is likewise lacking since the Rev. Thomas's personal papers were disposed of and his house destroyed after his death.