The winger missed almost all of last season with heel and hip injuries.
Fernandez – who made his first-team debut in a friendly against Royal Antwerp in Spain last year – returned to action in the summer.
The 21-year-old starred for the club’s Under-23s in last week’s 2-0 win over Sunderland – he won a penalty and scored Newcastle’s second goal – and he was handed another Premier League 2 start against Middlesbrough on Monday night.
Newcastle United transfer news: Magpies identify £40m James Maddison alternative with ex-Crystal Palace man linked
Eddie Howe’s surprise Newcastle United transfer admission as Brighton draw reinforces priority
Sunderland suffer major injury blow
Brendan Rodgers reveals he talked Swansea City defender out of move to Newcastle United whilst on Mount Kilimanjaro
Newcastle United transfer target confirms move ahead of official announcement
Fernandez, however, pulled up in front of the home dugout at Whitley Park in the second half. Fernandez was visibly upset when he limped off the pitch.
Coach Neil Redfearn said: “Just a little bit of tightness in his hamstring. One of the problems we’ve got with Victor, because his game’s very explosive – he has real pace and power when he goes past people – is just managing his minutes. Obviously, he’s had a lot of injuries.
“I thought he looked good again, but obviously we’ve got to look after him and make sure that eventually he can play 90 minutes comfortably, but I don’t think he’s at that point yet.”
Asked about the severity of the injury, Redfearn said: “It sounded like a bit of tightness when he described it, so we’re hoping that’s all it is.”
Meanwhile, Newcastle’s Under-23s will take on Aston Villa at Villa Park on Monday night (7pm kick-off).