The date of the first establishment of the Royal Malta Yacht Club cannot be ascertained, although there are rumors as to the existence of a yacht club in Malta as far back as 1835. It is, however, on record that the admiralty issued a warrant authorising the use of the Blue Ensign in 1873 (re-issued in 1894 and again in 1935). By 1892 the Club had reached its nadir and virtually ceased to exist.

About 1896, a small group of gentlemen resident in Malta and owning as a syndicate a 30-ton cutter called the "RHODA" formed an association which was commonly known as the "Rhoda Sailing Club".

At first their interests were primarily in cruising but, later on, races were staged for sailing dinghies and small local craft, which attracted other enthusiasts who were not members of the original syndicate. From these and others, a club, known as the Mediterranean Skiff Club, was formed in 1905 and the West of England Conference Dinghy adopted as its racing class. The Mediterranean Skiff Club remained in existence until 1916 when it was wound up owing to the majority of its members being on active service.

In 1921 the Club was reconstituted under the title of the "Malta Yacht Club" presumably in ignorance of the Royal Tradition it had inherited, and it was not until 1928 that steps were taken to obtain official recognition of the prefix "Royal" although some bolds previously the Admiralty had adopted that form of address when communicating with the Club. In 1929, following a successful motor-boat regatta, the Malta Motor Boat Club was formed and in 1930 the two Clubs were amalgamated under the title of the senior body, with the declared policy of providing a common meeting ground for the Maltese and English sections of the community, and to this end, of building premises suitable to the Club's activities.

It is important that these facts should not be lost sight of in the future, since they formed the basis of negotiations with the Civil Government for the grant of land upon which to build, and any avoidance of this undertaking may react on the welfare of the Club.

In August 1935, the Lords Commissioners of the Admiralty were pleased to grant to the Royal Malta Yacht Club the restoration of the former privilege of wearing the Blue Ensign.

 After the outbreak of the war with Italy in 1940 the Club ceased to function. A year later some of the keener members, reinforced by a few enthusiasts who had arrived to strengthen the garrison, recommended racing until the attacks of the Luftwaffe, not to mention the stifling effects of our own smoke screens, drove them out of the water. On 18th July 1942 a bomb completely demolished the Club House and many boats were lost or badly damaged.

It was not until 1944 that it was possible to get together sufficient people anxious to race and re-form the Club. St Rocco Baths were used as a temporary Club House until 1950. Boats which had been sold out of the Club were traced and bought back into the fold; hulls, sails and gear were rebuilt or repaired and racing was resumed, at first on a small but later on a steadily increasing scale. In 1945 the Annual Regatta was revived and Long Distance Dinghy Races held for the first time since the war. The Club House at Floriana (Hay Wharf) was rebuilt on its former site in late 1949 and the Club thereby duly re-established in its original premises.

 In 1952 Off-shore races for 30 and 50 square meter yachts were introduced and races to various ports in Sicily, Libya and Tunisia were held regularly. In 1968 the first Middle Sea Race was sailed and 1987 saw the start of the Rimini-Malta-Rimini race. In 1970 the Club moved from Hay Wharf, Floriana to Fort Manoel, Manoel Island. Fort Manoel, completed in 1726 by the French military engineer De Tigne, has a remarkably fine design and a most impressive gate, which is clearly visible from Marsamxett Harbour; originally the complex housed 500 soldiers. The Fort also commands a superb view of Valletta and the harbour. 

 In 1972 the ex-officio post of Commodore, formerly held by His Excellency, the Governor General, was regraded into President of the Club, and the post of Commodore assumed by the Chairman of the General Committee.

In 1975 the Club instigated the formation of the Malta Yachting Federation with a view to such body assuming the reception, at the time accorded to the Club by the Malta Government (National Sports Board), as the National Authority and Controlling Body for yachting in Malta.

In the years that followed the premises and activities remained unchanged with the Malta Syracuse Race and the Middle Sea Race becoming premier international events. The latter, which had been generously supported by the Martini International Club since 1972, became known as the Martini Middle Sea Race and in 1974 the associated race for non-IOR yachts became the Martini Ulysses Cruiser Race. In 1980 the Porto Cervo Race was inaugurated in association with the Yacht Club Costa Smeralda, and that year also saw the revival of an annual race to Tunisia, in co-ordination with the Port Authority at El-Kantaoui.

 In 1978 the Name of the Club was changed to the Valletta Yacht Club and the Maritime Flag of Malta became the ensign of the Club.

In 1970 the Club Premises which had been situated at Hay Wharf within Marsamxetto Harbour moved to the present premises on Manoel Island. Hay Wharf was retained for the Dinghy Section of the Club but was given up in 1982.

On the 13th November 1990, the Club reverted to the original name "THE ROYAL MALTA YACHT CLUB".

The Club was based at Couvre Port until November 2008 when the RMYC moved into the ex MMA Buildings in the Ta'Xbiex Yacht Marina.

The new Clubhouse underwent a nine month refurbishment program and was finally ready in October 2009.