It was a harsh lesson for the newly-promoted Cottagers who were never allowed to find any sort of rhythm.
City were ahead within 90 seconds of kick-off thanks to a fantastic piece of play by Fernandinho.
The Brazilian intercepted a poor pass on the halfway line and then drove forward before sliding a perfect cross into the path of Leroy Sane who tapped the ball into the net from five yards out.
The champions were quicker and sharper in every department in the opening stages as the visitors grimly clung on.
With 15 minutes played, City went agonisingly close to doubling the lead after a sublime piece of skill by Bernardo.
The Portuguese juggled a high ball to his feet before putting Raheem Sterling free and the England forward was unlucky to see his shot deflected onto the crossbar by the sprawling body of keeper Marcus Bettinelli.
But six minutes later, City were two goals to the good as the excellent Bernardo held off a challenge inside the box to play the ball to Aguero whose miscued shot was turned in off the bar by David Silva – his 50th Premier League goal for the Blues on his 350th appearance.
Sane was a shade unlucky to see another goal ruled out for offside on half-time, but the champions did score again, three minutes after the re-start.
Star man: Bernardo Silva
Almost exclusively, Bernardo Silva has played on the wing during his time with City.
The former Monaco playmaker was given one of the creative central berths alongside David Silva against Fulham and there were times when his skill and vision were breath-taking.
Already a big crowd favourite, he created numerous chances, worked tirelessly and was excellent from start to finish.
Delph, Sane and Otamendi take their chance
Though none of them had started a Premier League game this season, you’d never have known it.
Sane, Fabian Delph and Nicola Otamendi all impressed with displays that will have delighted Pep Guardiola.
Delph filled in for Mendy and rarely put a foot wrong, Otamendi was a commanding presence at the back and Sane opened his account for the campaign and saw another couple of efforts go close in an impressive performance.
Pep Guardiola reaction
"I said (in my pre-match press conference): I give a lot of credit to Fulham.
"They asked a lot of us and because they want to play, they will do a lot of surprises in this Premier League.
"That's why I give a lot of credit - 3-0 is a good result. We created a lot of chances to score five, six or seven goals and we have to be more clinical in those situations.
"The contenders are so tough and goal difference is important."
What it means…
Liverpool and Chelsea continued their 100% start to the campaign, so the Blues remain two points behind the top two in third.
Watford, the only other side yet to drop points, play Manchester United in today’s early evening kick-off.
City kick off the Champions League campaign against Lyon on Wednesday at the Etihad.
Then it’s off to South Wales to face Neil Warnock’s Cardiff City in the Premier League.