Guimaraes has been linked with Arsenal, with British media reporting that the Gunners had agreed a deal worth around 75 million pounds for the Brazil international. Neither club has confirmed the reported transfer.
Speaking during Newcastle's pre-season training camp in Spain, Wilson said selling Guimaraes was never part of the club's plans.
"We didn't want to sell Bruno. It wasn't in the plan to sell Bruno. None of us - or ownership - wanted to sell Bruno," Wilson said.
"He's our captain, he was very important to us, and the debate over his price - it's a world-record fee for a player of his age.
"What we had to weigh up was, very respectfully from Bruno with his behaviour towards us, very emotionally as well, effectively told us he wanted to leave and move on."
Guimaraes joined Newcastle from Lyon in January 2022 and quickly became one of the club's most important players.
The 28-year-old has made 195 appearances for Newcastle in all competitions, scoring 31 goals. He also captained the club to League Cup glory in 2025, helping them end a long wait for domestic silverware.
Wilson stressed that Newcastle had not planned for Guimaraes to leave this summer but said the club had to adapt to the situation.
"There's no part in saying (the transfer) was part of our strategy and was in our thinking this summer - it wasn't," Wilson said.
"But we have got to be flexible and react to things that happen.
"It might have been in our plan to sign one player, but we didn't get him so we move on to another. We can only be honest about that."
Guimaraes' potential departure would represent another major change at Newcastle following the exits of Anthony Gordon, Sandro Tonali and manager Eddie Howe.
Newcastle are due to begin their Premier League campaign against Liverpool on August 23.
