Second-half goals from Marcus Rashford and Marouane Fellaini were enough to see United through, and crush West Ham spirits in what was the final FA Cup tie to be staged at their Upton Park home.
Despite a late fightback from Slaven Bilic’s men, United held on to secure a 2-1 victory and the Dutchman was left in no doubt that they were the better team.
West Ham United 1-2 Manchester United
The Emirates FA Cup
Sixth Round replay
7pm, Wednesday 13 April 2016
Boleyn Ground, West Ham United FC
Winners receive £360,000 from prize fund
Live on BBC
"I think we deserved it," said Van Gaal.
"We controlled the game for 85 minutes and could have finished the game much earlier.
"They scored and made it very nervous, but David De Gea saved us with a fantastic save.
"But when you see the match, we have deserved it and had the bigger chances."
Rashford’s opening goal certainly caught the eye, with the 18-year-old flashing a shot past the helpless Darren Randolph to put the Reds ahead.
It was the latest strike from the England Under-20 striker, who has quickly become a key member of Van Gaal’s team following six goals in 11 games since his debut earlier this year.
And Van Gaal admits he hasn’t been too surprised with the youngster’s success, having worked closely with him in recent weeks.
"He is very focused on his work, I admire that," he revealed.
"When you are so young and with so much attention, it is not easy and he is scoring so many important goals.
"When you can cope with that attention and focus, when you have criticism, it is impressive. He can cope with it also and say sometimes, ‘Yes manager, you are right and I have to do this and that.’
"There are not a lot of players who can see their self-image in the match like he can.
"It was a great goal - I was behind the view and I shouted ‘shoot!’
"But to do that is much more difficult. It was a very great goal, but I have told him that when you are 60 metres out, you have to dribble and take a shot.
"He has that ability and he can score a lot of goals."
United will now take on Everton on Saturday 23 April in the first of this season’s Emirates FA Cup Semi-Finals at Wembley.