The defender, 25, who spent two years at Craven Cottage, will officially join the Lions when his Fulham contract expires at the end of the month.
"Coming to work at a place where you are so wanted is a great feeling," he told the Lions' website.
"I can't wait to get going and am looking forward to putting on the Millwall shirt."
Newcastle-born Hutchinson made 121 league appearances for Motherwell before Fulham signed him from the Scottish side after a number of clubs - including Millwall - had shown an interest in him.
However, he struggled to establish himself as a first-team regular, making 34 league appearances during his time in west London.
"Shaun is a player that as a club we have been aware of for quite a period of time," said Millwall manager Neil Harris.
"We tracked him diligently when he was at Motherwell and when he was moving down south we bid for him.
"We monitored him last season knowing that he was coming out of contract.
"He is a no-nonsense defender who likes to head it in both boxes and is very aggressive in his approach."
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Shaun Hutchinson has agreed a two-year deal with League One club Millwall after his recent release by Fulham.