In March 1636 Charles I entrusted Juxon with important secular duties by making him Lord High Treasurer of England as well as First Lord of the Admiralty; for the next five years he had to deal with many financial and other difficulties. He resigned the treasurership in May 1641. During the Civil War, the bishop, against whom no charges were brought in parliament, lived undisturbed at Fulham Palace. His advice was often sought by the king, who had a very high opinion of him. The king selected Juxon to be with him on the scaffold and to offer him the last rites before his execution.