Wogan was the son of Sir John Wogan, who was MP for Pembrokeshire and High Sheriff of Pembrokeshire. In 1646 Thomas Wogan was elected MP for Cardigan Boroughs. During the Second Civil War, he fought on the side of Parliament at the Battle of St Fagans in 1648. After this battle, he was awarded some of his arrears of pay, promoted to Colonel and appointed governor of Aberystwyth Castle.