Kelly has guided the Foxes to six wins in the nine games he has managed since he took over from Craig Levein.
But this win was by no means comfortable and Millwall can consider themselves unlucky but they remain in a relegation dogfight to maintain their Championship status.
Hughes' goal came in the 31st minute when Leicester caught Millwall napping.
Iain Hume played a smart pass into Hughes who neatly lobbed goalkeeper Andy Marshall from just 12 yards out.
There were earlier warning signs for the struggling side when both Hume and the lively Matt Fryatt had chances in the opening few minutes.
Hume was denied by some desperate last minute defending from Matt Lawrence while Fryatt burst through the Millwall defence only to be stopped by the referee's whistle for being offside.
Joey Gudjonsson also had a chance to give Leicester the lead just three minute before Hughes' strike.
The midfielder, playing his last season in England after deciding to move back to Holland, struck a sweet free-kick from 30 yards which cannoned off the underside of the crossbar before bounding clear.
Millwall hustled and for moments looked sure to find a way back into the game, largely thanks to some poor goalkeeping from Leicester's Paul Henderson.
He first made a meal to tip a harmlessly looking cross over the bar. He then flapped at Alan Dunne's free-kick which fell kindly for Marvin Elliott, but his shot hit the post.
Spirited Millwall were resurgent after the break. First David Livermore's free-kick was well saved by Henderson on 50 minutes.
Substitute Marvin Williams then went on a surging run two minutes later and was only stopped after a challenge from three Leicester defenders as referee Mike Thorpe waved away appeals for a penalty.
Henderson was then called upon to pull off a close range save to deny Paul Robinson who jumped highest to meet Livermore's corner.
Dunne was again causing problems for Leicester. He first had a shot from the edge of the area which narrowly sailed over the bar.
He then played a teasing cross into the box which Henderson missed, but the goalkeeper's blushed were spared as the ball drifted out for a goal-kick.
Barry Hayles nearly marked his return from injury with an equaliser as Millwall pressed to draw level.
The former Fulham striker raced though the Leicester defence but was eventually wrestled to the ground. But once again Mr Thorpe turned down Millwall's appeals for a spot-kick.
Despite Millwall's pressure they were unable to find a way through and remain deep in a relegation battle, while Leicester's good form continues.