Crabtree, 22, will get a six-year deal, ESPN reported Wednesday, that he can trim down to five years if he meets certain performance clauses.
The deal came during an early-morning meeting Wednesday between Crabtree and his agent, Eugene Parker, 49ers owner Jed York, General Manager Scot McCloughan and Paraag Marathe, the team's VP of operations.
The Press Democrat's Matt Maiocco reported the deal via Twitter at 4 a.m. then followed with a tweet of the six-year signing.
The former Texas Tech star is the only draft pick who has yet to sign, so this meeting could point to progress in him ending his contract impasse.
He is expected to report to the team's training facility Wednesday.