During his time in the mayor's office, he oversaw massive growth in Jacksonville. He promoted the city around the world in an attempt to lure international investments and to get corporations to relocate offices to the city. He commissioned the production of a slide show called "The Jacksonville Story", hundreds of audiences saw it around the world. The American National Exhibit showed a film version in the Soviet Union. Burns personally made presentations at The Hague and in Israel. He made "The Jacksonville Story" known from coast to coast, and so was Jacksonville's mayor.
He was elected president of the U.S. Conference of Mayors, president of the Florida League of Municipalities, and delegate to the International Congress of Municipalities. While mayor, he won tax breaks for insurance companies and Prudential Insurance relocated from New Jersey to a skyscraper in Jacksonville. Other insurance companies followed, and Jacksonville became known as the insurance capital of the South.
A new courthouse and City Hall were built on the site of rotten wharves, and a long-promised Civic Auditorium was built on the river. Jacksonville Memorial Coliseum and Sam W. Wolfson Baseball Park made the city thoroughly modern. The Atlantic Coast Line Railroad, today CSX, moved from Wilmington, North Carolina to the Jacksonville riverfront. The world's largest Sears Roebuck store opened on what once was skid row. A modern expressway system took shape and the city got the Jacksonville Suns baseball franchise and a hockey team.
The city faced many problems during Burns' term. Racial violence ignited on August 27, 1960 during a protest to integrate downtown lunch counters in the Hemming Park shopping area. Segregationists responded by attacking the protesters with ax handles; the day is remembered as "Ax Handle Saturday." Burns tried to blame the ax handle riots on visitors but the police chief attributed the attacks to locals. The city's police department was ridden with scandal and multiple grand jury indictments were handed down on public officials all around him.
One of his final acts as mayor was his handling of the Hotel Roosevelt fire in downtown. With his quick action, he saved most of the hotel visitors from possible death from smoke inhalation. He left the mayor's office in 1965 to become governor of Florida.
The 1966 gubernatorial elections pitted the sitting governor against Robert King High, a popular Miami politician. This primary was significant because Burns represented the conservative wing of the Democratic Party and King was the choice of the liberals from South Florida. Governor Burns lost the 1966 Democratic primary; he avoided supporting King in the general election. Political observers in Florida point to King's supposed failure to seek such endorsement from Burns. This left the party divided in the face of united Republican support for Claude Kirk. He left office on January 3, 1967 as the first Democratic Governor of Florida in history to be succeeded by a Republican.
Jacksonville's main public library, built in 1965, was named the Haydon Burns Library in honor of the former mayor. It was designed by Taylor Hardwick, a local architect who designed many local structures built in Jacksonville. However, it too was replaced in 2005 by a new Main Library.
In 1966, the building located at 605 Suwannee Street in Tallahassee, Florida opened and was named the W. Haydon Burns Building. It became home to the State Road Department, now the Florida Department of Transportation.
In 2004, the city of Jacksonville renamed the old City Hall, built by Burns, the Haydon Burns City Hall Annexe.