The company has worked with the WPP agency in the UK and in India since 2014. The business will be run by MEC New York, with support from the San Francisco office.
Initiative, the Interpublic group shop, is the incumbent on countries outside of the UK and India.
Phil Bienert, the chief marketing officer and executive vice president of digital commerce at GoDaddy, said: "Our decision to move GoDaddy's media business to MEC is a natural step as GoDaddy expands our business globally.
"We looked for a strong partner with local media expertise and global technology and tools to help drive forward our efforts to reach small businesses at the right time with the right medium.
"MEC shares our passion and vision for delivering locally-relevant, targeted messaging to connect with people worldwide."
In November GoDaddy named TBWA, the Omnicom agency, as its first global creative agency after a competitive pitch. This account is also being run out of TBWA’s New York office.