Guimaraes, who is currently on international duty with Brazil, is said to be a target for a number of Premier League clubs, including Arsenal.
However, on Wednesday, The Athletic reported that it was struggling Newcastle, which is looking to make big moves in order to boost its Premier League survival bid under Eddie Howe, which had made big inroads in a deal for the 24-year-old.
The Athletic's report stated that Guimaraes would undergo a medical in South America in order for the transfer to go through.
Numerous other outlets, then reported that Newcastle were closing in on securing the transfer, though stopped short of stating a medical would soon take place.
Yet Lyon has now issued a statement denying any speculation that an agreement had been reached.
"Olympique Lyonnais categorically denies the false information disseminated by many media reporting an agreement between Newcastle and OL for the transfer of Brazilian international midfielder Bruno Guimaraes," the statement read.
"In this transfer window period where the slightest rumour is often presented as reality, Olympique Lyonnais reminds that only information officially released by the club is to be taken into consideration."
Guimaraes joined Lyon from Athletico Paranaense in January 2020. He has gone on to make 56 appearances in Ligue 1, scoring three goals. s
He also has an Olympic gold medal to his name, having helped Brazil defend their crown in Tokyo last year.
Newcastle have made two signings in January, bringing Kieran Trippier back to the Premier League from Atletico Madrid, and drafting in Chris Wood from relegation rivals Burnley.
The Magpies are also attempting to sign a centre-back, though have so far been frustrated in their attempts to bring in Sevilla's Diego Carlos, while on Wednesday, reports claimed Brighton and Hove Albion had turned down an approach for Dan Burn.