Matoya was designed by A.M. Coulson and constructed by J. Husk & Son in Wivenhoe. Initially operating on the upper Thames, the vessel was acquired by Douglas Tough's watermen for service at Dunkirk during World War II. Records indicate a crew of three—J. Jameson, L. Milson, and A. Crump—presumably civilians; however, no log of Matoya's activities during the evacuation has survived.

Following the Dunkirk evacuation, Matoya continued in wartime service on yacht patrol. During this period, she sustained damage while transferring crew to a drifter, which subsequently struck a mine and exploded. As a result, Matoya lost her propellers, rudder, and part of her keel. The vessel was later reported as serving as an auxiliary fire float on the Thames.

After the war, Matoya was found almost derelict in Ramsgate harbour. She was purchased and extensively rebuilt, both internally and externally, by Mr. and Mrs. Dinniwiddie. To facilitate repairs to her transom while afloat, they shifted two tons of ballast into her forepeak, causing the stern to rise out of the water for easier access.

Matoya had two subsequent owners before coming under the care of Bill Finch, a dedicated member of the Association of Dunkirk Little Ships (ADLS) and former owner of Ryegate II. Finch prepared the vessel to participate in the 1985 return to Dunkirk.

In 1988, while en route to Ostend at the start of a journey through the Dutch canals, Matoya struck a submerged object, causing her seams to open. The Dover lifeboat responded and assisted the vessel.

Matoya is featured individually in a series of stamps titled Little Ships of Dunkirk, issued by Palau in 2015 to commemorate the 75th anniversary of Operation Dynamo.