The Old Trafford club is set to pay £64 million ($82 million) plus another £8m ($10m) in add-ons for the 20-year-old Denmark striker. He will become Erik ten Hag's third summer signing following the arrivals of Mason Mount and Andre Onana.
Höjlund emerged as the top centre-forward target after the decision to back away from moves for Harry Kane and Victor Osimhen. Ten Hag was initially keen to add an experienced No. 9 to his squad, but sources have told ESPN that the Dutchman has come round to the idea of working with youngster Höjlund because of his potential.
Atalanta had demanded £77m for Höjlund while United, at one point, were firm in their stance that they would not pay more than £60m. United weakened their position and agreed to pay more than first expected because of an acceptance that a striker had to arrive before the deadline.
Meanwhile, Atlanta signed forward El Bilal Toure on Saturday, paving the way for Höjlund's departure.
Ten Hag's team was the lowest scoring side in the Premier League's top six last season with 58 goals. Höjlund is one of Europe's best young players albeit he is so far unproven.
Höjlund is yet to play 100 senior games in his career and last season scored nine times in 32 appearances in Serie A. He's scored 27 goals in his senior career during spells at Copenhagen, Sturm Graz and Atalanta and has six in six appearances at international level for Denmark.
His arrival will take United's summer spend close to £180m, and the club will now have to work on departures to balance the books. Anthony Elanga has joined Nottingham Forest in a deal which could rise to £20m, and Alex Telles has joined Al Nassr for £4m.
United will also listen to bids for Scott McTominay and Harry Maguire, who was recently the subject of a rejected bid from West Ham United, but it will take a large offer before they are allowed to leave Old Trafford.