Guedes played in Valencia's dramatic 1-1 draw with LaLiga leader Barcelona on Monday but the Portuguese star will go under the knife to prevent further damage.
The 20-year-old has been a revelation since joining Valencia from Paris Saint-Germain on a season-long loan.
Guedes has scored three goals and claimed five assists to help Valencia make an unbeaten start to the campaign in second position, four points adrift of Barca.
Valencia defender Ezequiel Garay will also undergo an MRI scan after suffering a side injury at home to Barca.
Garay, 31, was forced from the field with four minutes remaining.