Docherty was recruited to Brisbane from Gippsland Power with pick 12 in the 2011 National Draft.
The 20-year-old made his AFL debut in Round 4 this season and went on to play 13 games, including 11 of the Lions' last 14 matches.
A life-long Carlton supporter, Docherty had expressed a strong desire to return to Victoria.
Carlton’s GM-Football Operations Andrew McKay says the silky-skilled half-back is a terrific addition for the Blues.
“It’s fantastic to pick up a quality player who has been a Carlton supporter all his life,” McKay said.
“Sam is someone who will add to our list, to help us improve next year.”
Docherty says he’s rapt to be back in Victoria, and is excited about playing alongside footballers he has grown up admiring.
“I can’t wait to put the jumper on, it’s a dream come true,” Docherty said.
“Obviously growing up (barracking) for them and now getting here – I can’t think of anything better.”