Lowther was a commissioner of array for Cumberland and Westmorland in 1642. He was commissioned a colonel by the Royalists during the Civil War and was Governor of Brougham Castle until 1644. However, he claimed not to have borne arms against the Parliamentarians, and took the Covenant when their forces approached. He was recommended to continue as a justice of the peace for Westmorland (having sat on the bench since 1641) and was fined on relatively favourable terms. He did not continue as a justice or in the recordership of Kendal after 1648, during the Interregnum.