Against a disappointing Charlton side, Emerton's 41st minute header when he ghosted in at the back post was enough to secure the three points and ensure they bounced back from Saturday's last minute defeat to Aston Villa.
Blackburn boss Hughes was pleased with his side's performance and felt they were full value for the victory.
"We really deserved the three points today," he said. "It was important psychologically to win and it is vital to have consistent home form that gets us points."
Indeed before today Blackburn had only won once at Ewood Park all season, Hughes' first game in charge back in September was a similar 1-0 success over Charlton.
"It was crucial to score first today and I was delighted we went in at half-time a goal up. We came under pressure at the end but withstood it and were good value for the win."
As for Charlton, this match seemed a game too far for Alan Curbishley's men after a hectic Christmas period threw up four games in the space of nine days.
"We never got going today," Curbishley admitted. "Perhaps this was one game too many but we had no spark and fizzled out after ten minutes.
"I am disappointed because we are better than we showed today but Blackburn probably deserved the three points."
The home team certainly ensured Charlton keeper Dean Kiely was kept warmer than his counterpart Brad Friedel at the other end with Jonathan Stead desperately unlucky not to get his first goal of the season.
Blackburn's hero from last season hit the bar at Bolton last week and cannot seem to buy a goal as an inspired Kiely denied him on at least three occasions.
His first chance came midway through the first half after Paul Dickov had forced the Irish keeper to turn his low shot round the post.
Emerton's delivery was good, Dickov saw Danny Murphy block his header on the line and then Stead following up with foiled by a superb save from Kiely.
He then headed over Dickov's right-wing cross, but four minutes before the break Emerton showed him how it was done.
The Australian winger found space at the back post and when David Thompson swung in an excellent cross he was in the right place to guide a header back beyond Kiely.
In the first half Jerome Thomas posed Charlton's only real threat and it was his shot that carved open their only real chance seconds before the interval.
After leaving Thompson for dead his scuffed effort came all the way to Jonatan Johansson, but Friedel was down quickly to make a one-handed stop.
Blackburn countered rapidly; Stead muscling Talal El Karkouri off the ball but Kiely turning away his fierce drive.
After the break Curbishley withdrew the dangerous Thomas and despite the arrival of Jason Euell, Charlton's threat seemed to diminish.
Kiely remained the busier of the two keepers as Stead forced him into a low save from a tight angle and then Thompson tested his reflexes with a free-kick.
As the minutes ticked away, the Addicks finally applied some pressure to the Blackburn goal with a succession of corners and dangerous crosses, but the home defence held firm, much to the relief of the home fans.