The 14-year-old was available for free due to Bolton's financial woes but the Premier League champions have paid an initial fee and included bonuses.
Manchester City have signed young striker Daniel Ogwuru from Bolton for around £100,000.
City have long held an interest in the 14-year-old and had their initial bid of the same value rejected back in January.
Ogwuru since became available for free as a result of Bolton’s financial problems and subsequent administration.
A number of clubs had made approaches to the youngster’s family as a result, but City have gone back to Bolton’s administrators with their original offer, which covered their obligations regarding training fees set out by the league’s Elite Player Performance Plan regulations.
City’s offer also includes a number of performance-related add-ons that will apply to Ogwuru’s time with the club’s various youth teams. Should he reach the first team in the future, Bolton could receive a seven-figure sum.
Ogwuru has been monitored by England scouts with a view to capping him at youth level in the coming years, and City plan to put him straight into their Under-15 team for the age group’s upcoming campaign.
He has caught the eye of scouts across the north west in recent months, with his size and poise in front of goal helping him stand out.