Sheikh Mohammed's royal blue Godolphin silks have been carried to victory in the Epsom Derby for the first time with Masar causing an upset in the premier Classic.

Trained by Charlie Appleby, the 16-1 chance was ridden by William Buick on Saturday (Sunday AEST) to beat Dee Ex Bee with Roaring Lion third and the favourite Saxon Warrior fourth after striking trouble in the run.

Sheikh Mohammed was understandably thrilled with the result.

"It's not easy to win the Derby, but we have won it. We are pleased to be here today," he said.

"Charlie Appleby is a very good trainer and the horse came from Dubai."

"I was jumping up and down in the final furlong.

"Horses are in my blood, I love them."

The win was also a first in the Derby for Appleby who had been upbeat about the colt's chances after his third in the 2000 Guineas won by Saxon Warrior.

"It's not sunk in yet. It still feels a dream," Appleby said.

"I'm delighted for His Highness Sheikh Mohammed. Firstly for giving me the position to be here. I've always said when I started this job I wanted to be the first person to have a Derby winner in Godolphin blue.

"It's a fantastic team effort. Brett Doyle rides him every day.

"He said he would stay and William has given him a peach of a ride."

Dee Ex Bee runs in the colours of Sheikh Mohammed's son, Sheikh Hamdan bin Mohammed Al Maktoum.

"We came here with doubts about his effectiveness on the track and I'm not sure it suits," trainer Mark Johnston said.

"Because of the camber he rolled on to the one on his inside, but he rallied again up the hill so it bodes really well for the future.

"You could go to the Irish Derby, but I've said before that I don't think I've ever had a horse more suited to the St Leger, so I think it could be best to work backwards from that."