Shaun, 29, switched to The Den from MK Dons, for whom he made a total of 137 appearances and scored 25 goals.
The Irishman was one of then manager Ian Holloway's first signing and played a pivotal role in Millwall's successful battle to beat the drop in 2013/14.
Williams, who can play in midfield or at centre-half, was again a prominent figure throughout the 2014/15 campaign, making 39 appearances before his season came to a premature end after picking up a foot injury during a 2-0 win over Wigan in April.
He was virtually a mainstay in The Lions' midfield last season, making 41 appearances, until a red card at Coventry City in April kept him sidelined through suspension. The performances of young talent Ben Thompson during Shaun's suspension restricted the latter's contribution thereafter to that of a substitute.
The battle for a midfield berth during the coming campaign promises to be an interesting one.