On his return in December 1685 his friends were desirous that he should enter the Royal Navy, but it was not till January 1687–8 that he was received as a volunteer on board the Mary, the flagship of Sir Roger Strickland.

Within a few weeks after the accession of William III and Mary II, Fairfax was promoted to be lieutenant of the Bonaventure, commanded by Captain (afterwards Sir) Thomas Hopsonn.

In June 1693 Fairfax was moved into the Pembroke of 60 guns, and, returning in her to England, was appointed to the command of the Ruby, a 48-gun ship, ordered to cruise on the coast of Ireland for the protection of trade.

While on this service he had the good fortune to capture, after a hard-fought action, the Entreprenant, a French privateer of the same nominal force, but larger, and with a more numerous complement.

On returning from the Baltic he was appointed to the Cambridge, and in January 1701 – 1702, on the eve of the declaration of war, was transferred to the 70-gun ship HMS Restoration, one of the squadron which sailed under Sir John Munden in May.

After failing to intercept the French squadron off Corunna, Munden and his ships returned to Spithead, and in the following autumn Fairfax was sent out to reinforce the grand fleet, which he joined at Vigo on 18 October, too late to share in the glory or the treasure, but in time to take part in the labour of refitting the prizes and bringing them to England.

With this the Berwick continued during the summer and was one of the six ships which vainly chased a French squadron off Cape Palos on 8 May - a failure for which Fairfax and the other captains were tried by court-martial, but fully acquitted.

He was one of the division actually engaged under Byng at the reduction of Gibraltar (23 July), for his share in which exploit ‘the Queen afterwards presented Fairfax with a silver cup and cover bearing a suitable inscription, which is still preserved by his descendants’.

Her marines were landed for service in the trenches and Fairfax himself had command of the seven bomb vessels, whose terrible fire cowed the garrison and rendered the approaches of the besiegers easier and safer.

It was then cancelled, and Lord Dursley, who was much his junior, was, by the political interest of his family, made Vice Admiral of the Blue in his stead, with seniority of 10 January.

Prince George obtained for him a commission as rear-admiral, and half-pay equal to that of the rank which he had been deprived of and on 20 June 1708 had him nominated a member of the Council of the Lord High Admiral.