The rapper will serve his sentence in city jails, not a state prison. He could be released in about eight months with good behavior.
Before Monday's court appearance, it had proved difficult to actually begin Lil Wayne's agreed-upon sentence.
First, the rap star's sentencing was postponed in February so he could undergo surgery on his bejeweled teeth. Then, a fire shut down Manhattan's main criminal courthouse while he was on his way there last week.
Lil Wayne has been one of music's most prolific and profitable figures in recent years. His "Tha Carter III" was the best-selling album of 2008. His latest album, "Rebirth," was released last month.
Facing jail with his career in full throttle, Lil Wayne has prepared with a burst of work and farewell shows and videos for fans. He said in a video clip sent last week to MTV News that he shot footage for seven music videos with various artists in one night over the weekend.
He told Rolling Stone for a story last month that he planned to keep working while behind bars.
"I'll be still rapping in there, have a gang of raps ready when I come back home," he said.
With good behavior, he could be released in about eight months.
City jail officials haven't said where the multiplatinum-selling artist will be housed among their roughly 13,000 inmates. His lawyer has said she plans to ask for protective custody out of concern for his safety and health following his extended oral surgeries.