The 19-year-old, on loan from La Liga champions Barcelona, was carried off on a stretcher at Goodison Park in the second half of the win which allowed Everton to move into fourth in the Premier League.
"It doesn't look great, it's a soft tissue injury, he pulled his hamstring," Everton manager Roberto Martinez told the BBC.
"We will do the scan straight away, he felt it and we will assess it, he is like a sprinter and the hamstrings are exposed in those sort of injuries."
The Spain under-21 forward has hit his stride in recent weeks, scoring his first goal for the club in the 4-0 win over Stoke late last month and netting a stunning equaliser in the 1-1 draw with Arsenal on Sunday.
His impact his mirrored the form of Everton, who now sit just four points off leaders Arsenal following their defeat to Manchester City.
They left it late against Fulham, however, with Leon Osman's opener being cancelled out by a Dimitar Berbatov penalty in the 67th minute.
"It was a really difficult game and the big moment was the penalty," Martinez told Sky Sport.
"After they scored we were more open-minded and it is great to score in games like this.
"Fulham were good and pressed with plenty of energy but we found a way to win and we have three very important points."
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