The 48-year-old Dutchman guided his former club Ajax to four consecutive Dutch league titles but less successful stints followed at Inter Milan and England's Crystal Palace.
In announcing last October that he was leaving Atlanta, Martino said the grind of a club campaign kept him from going home as much as he wanted. But he has been linked to the Mexican national team.
De Boer takes over on January 1 with United set for a pre-season match January 14 and a CONCACAF Champions League campaign that begins in February.
"The club's sportive ambitions, as set out in a long-term strategy to be the best in class, clearly fits my personal ambitions," de Boer said.
"I would like to build on the current success to develop a secure, solid foundation for the club at the top of MLS and beyond."
De Boer lasted only 85 days at Inter Milan after losing four of five Serie A matches and was gone after 10 weeks from Crystal Palace after a 0-4 start in the 2017-18 Premier League.
"Frank de Boer has a distinguished background, both as manager and player, and we're ecstatic to welcome him to our club," Atlanta United president Darren Eales said.