His official career was a very brilliant one, and deservedly so from the integrity of his work, from his application, despite frequent immoderation in partaking of wine, and from his business-like methods of work.

As Commissioner for the Affairs of Tangier and Treasurer, he visited Tangier officially.

He twice became Secretary to the Admiralty, and was twice elected to represent Harwich in Parliament, after having previously sat for Castle Rising.

He was also twice chosen as Master of the Trinity House, and was twice committed to prison, once on a charge of high treason, and the other time (1690) on the charge of being affected to King James II., upon whose flight from England Pepys had laid down his office and withdrawn himself into retirement.

Elected a Fellow of the Royal Society in 1665, he attained the distinction of being its President in 1684.