Several clubs are showing interest in the academy coach amid a wider summer of upheaval at the Etihad, says the Manchester Evening News.
Wilkinson took over the Under-21 role from Brian Barry-Murphy in 2024, after Barry-Murphy left following three seasons to pursue his own coaching ambitions. Barry-Murphy went on to work as Leicester's assistant before taking the Cardiff job last season, winning promotion from League One at the first attempt.
Barry-Murphy himself had taken over the City Under-21 post from Enzo Maresca, who is set to be confirmed as Pep Guardiola's successor at the Etihad following spells in charge of Leicester and Chelsea.
Wilkinson, son of former Leeds manager Howard Wilkinson, joined Manchester City from Sheffield Wednesday's academy in 2018. He spent two years as an Under-21s assistant before taking charge of the Under-16s in 2020 and the Under-18s a year later.
Three seasons at Under-18 level brought two league titles and the FA Youth Cup, with Wilkinson also playing an integral role in the development of Nico O'Reilly as he broke into the first team under Guardiola.
Moving up to the Under-21s in 2024, Wilkinson's side won the league in his first season in charge and reached the semi-finals this year with a new group of players. Six more youngsters made their first-team debuts for City this season, while O'Reilly was named the Premier League's Young Player of the Year.
Having seen the work Wilkinson has done with the Under-21s, he now has head coach interest from clubs in League One and abroad, while several Championship clubs are keen on bringing him in as an assistant coach.
City have already said goodbye to Guardiola and almost all of his backroom staff this summer, with set-piece coach James French the only member of his team confirmed to be staying on. Maresca is expected to bring in his own staff, meaning Wilkinson's departure would create a further significant gap in City's coaching structure.