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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, Oliver Cromwell promoted him to Colonel and appointed him as governor of Aberystwyth Castle.
An enthusiastic supporter of the army, he was appointed a commissioner of the High Court of Justice at the trial of King Charles. He attended every day  and in January 1649, was 52nd of the 59 signatories on the death warrant of the King.
After the Restoration of the Monarchy in 1660, Wogan was on 6 June 1660 excepted from the Act of Oblivion (ie exempted from the general pardon for King Charles's enemies). He surrendered on 27 June 1664 and was imprisoned. Held in York Castle, he managed to escape on 27 July 1664 and flee to the Netherlands. The last record of him dates from 1666 and has him in Utrecht plotting, with Edmund Ludlow and Algernon Sidney, against the English government.