Hayne, after surviving what was a rookie season of highs and lows, was handed Kelly's new playbook on April 4, the first day of the team's off season program.
On Sunday he had an epiphany.
Kelly's new high-speed playbook suddenly clicked in his head.
"It was weird because I was studying from Monday to Thursday and I was just like, 'I'm going to have a day off to just clear my head'," Hayne said.
"I did that and come Saturday I was OK.
"Then Sunday I just went, 'boom boom boom'
"It felt great because I've learned the majority."
Hayne's second year at the 49ers will be played under an almost completely different coaching staff, with just running back coach Tom Rathman surviving mass sackings after last year's poor season.
Hayne was cagey when asked if Kelly would again use him as a running back and a returner on special teams or in a completely different position.
"You'll have to ask Chip," Hayne said.
Despite cracking the playbook code, Hayne joked he might still need to stuff a cheat sheet in his pants.
"I've thought about it," he laughed.