On March 15, 1932 the Merced City Council accepted title to the site of an airport as a gift from the Twenty-Thirty Club and the Crocker-Huffman Company. The airport, an airstrip and 66 acres (0.27 km2) of land 3 miles (4.8 km) northwest of the city near the intersection of U.S. Route 99 and California State Route 59, was dedicated on April 3, 1932. The airport site was leased to George Voight for a term of five years, and a subsidiary airline of the Stinson Aircraft Company started Merced's first scheduled airline service. In May 1936 the City of Merced assumed responsibility for the airport; constructing buildings, hangars, and other improvements; expanding the site to 123 acres (0.50 km2).

In 1940 as the U.S. Army was trying to establish a 30,000 per year basic pilot training facility in the Merced area, Merced Municipal Airport was deemed unsuitable for a major training facility due to lack of room. The United States Department of War would ultimately select an area 2 miles (3.2 km) northeast of Atwater, now the site of Castle Airport, for its Air Corps Basic Flying School. That year, land the Merced Regional Airport now occupies in southwest Merced near Childs Avenue was acquired from delinquent tax rolls. The city council approved the first phase of construction of a new airport shortly after the acquisition. This new city owned airport would be known as "New Merced Municipal Airport".

In 1941 construction delays at the Air Corps Basic Flying School site forced the Army to lease the original Merced Municipal Airport, resulting in the first aircraft assigned to the Air Corps Basic Flying School being stored at Merced Municipal Airport and giving the Basic Flying School its first usable axillary field. After the United States entered World War II, the Civil Aeronautics Authority assumed responsibility for the final phase of construction of the New Merced Municipal Airport. By 1942 the new airport and its two runways; 6/24 and 12/30 each 4000' by 150', was completed by the United States Army Corps of Engineers working under the CAA.

In 1943 New Merced Municipal Airport was leased to the U.S. Army Air Force, becoming the sixth axillary field for Merced Army Airfield (present day Castle Airport). Under the lease, the airport's name was changed to "New Merced Municipal Airport Auxiliary Field". The lease was terminated immediately after the war, and the airport was returned to civil control. In the fall of 1945, the City of Merced sold the original Merced Municipal Airport site near Santa Fe Drive to the Chamber of Commerce for $7,500, leaving New Merced Municipal Airport (near Childs Ave) as the city's primary airport.

In 1946 United Airlines built offices and a terminal building and began one Douglas DC-3 flight each way a day. That year damage incurred during the Army Air Force's use of the site was repaired, and more improvements were made using federal funds. In 1948 Merced Municipal Airport was annexed to the City of Merced.

During the 1950s the airport was used to service United States Armed Forces aircraft, and a land acquisition in February 1955 allowed runway 12/30 to be extended. In 1967 runway 6/24 and its parallel taxiway were closed, and in 1975 a control tower was built.

United's DC-3s were replaced by Convair 340s, then Douglas DC-6s, then Boeing 737-200s in 1968-69. United flights to Merced ended in 1979.

On March 6, 2009 the city council voted to change the name from Merced Municipal Airport to Merced Regional Airport. In 2021, the city council voted to change the name from Merced Regional Airport to Merced Yosemite Regional Airport. In 2021, Advanced Air received a second Essential Air Service (EAS) contract for the City of Merced to provide commercial airline service to Harry Reid International Airport and Los Angeles International Airport. In 2023, the city council voted to change service from Los Angeles International Airport to Hawthorne Municipal Airport.

In December 2023, the airport broke ground on a $17 million dollar terminal replacement project. The new terminal is slated to be 11,000 square feet, up from 5,000 square feet in the current building.

Fly-In

Between 1957 and 2007 Merced Regional Airport hosted the annual Merced West Coast Antique Fly-In. Each year the fly-in drew hundreds of pilots from across the western United States to Merced to display their rare and antique aircraft. The fly-in featured an air show and an antique car show. In 2007, the 50th annual fly-in drew nearly 400 planes and several stunt pilots. Since 2008 the Merced West Coast Antique Fly-In has been canceled due to lack of sponsors and volunteers.