Having gone ahead through Leon Osman's 18th-minute goal the Toffees failed to press home their advantage and Dimitar Berbatov equalised from the penalty spot midway through the second half.
However, just when it seemed the visitors were threatening a winner Seamus Coleman, Gareth Barry and Kevin Mirallas all scored in the last 17 minutes to make the scoreline look somewhat harsh on the Cottagers.
Martinez felt his side suffered after a significant victory at Old Trafford and a well-deserved draw at Arsenal last weekend.
"It wasn't one of our best days. I was a bit fearful before the game as mentally we were going to be fatigued after the two away games which were very demanding," said the Spaniard.
"Physically we were fine but mentally the way we moved the ball it wasn't as sharp as usual, we couldn't see our normal patterns going forward.
"The first half we controlled the game and had we scored the second goal (earlier) it would've changed the game.
"Second half you have to give great credit to Fulham. They were well organised, pressing us high up, stopping us from playing.
"Once you get that equaliser I have seen many times before the home team collapse and you start panicking and you lose the game.
"What we did really well was the mindset changed. We didn't have anything to lose, we just wanted to win the game and we were brave, adventurous and creative in the final third.
"I don't think it was a 4-1 performance but we deserved the three points."
The only downside was a hamstring tear to youngster Gerard Deulofeu which is likely to rule him out for several weeks.
"Gerard is the big negative. He is a sprinter and those players are exposed to those injuries and he has pulled his hamstring," said Martinez.
"We don't know how big the tear is going to be but we expect Gerard to be out for some time.
"It is unfortunate because I thought he was ready to play a big role in the side but we are going to have to be patient and wait for him to come back in the final third of the season as strong as he can be."
Fulham boss Rene Meulensteen was in full agreement with Martinez about the scoreline flattering the hosts.
"I do think it didn't reflect the actual game," said the Dutchman.
"I thought we came back really strongly in the second half, changed a few things, put them under pressure, and that resulted in a few early chances.
"We got the equaliser and then conceded too soon after. That took the wind out of our sails.
"The 3-1 settled the game from that corner. We spoke about it, to concede another for 4-1, it didn't reflect the game."