George Blackstock claimed he was twice given a punishment in the 1980s involving Deep Heat smeared on a glove by the goalkeeper, when he was aged 16.
Mr Blackstock, 45 and from Belfast, tried suing the club and Mr Fox in a civil case for loss of earnings.
But his claim was unsuccessful and he must now pay out £200,000.
Preston County Court heard the two alleged assaults happened between 1986 and 1988 while Mr Blackstock, a midfielder, was held down by up to three other first team players.
He said he was given the punishment once for delivering the first team players cold tea and another time for calling a bad decision on the pitch.
Deep Heat is a type of muscular pain relief ointment.
The warehouse supervisor had tried suing for loss of earnings of £170,000 on the basis he would have played at least at Conference level for five years after leaving the club, but for the alleged assaults.
He claimed the alleged assaults led to a deterioration in his form on the pitch  and caused him post-traumatic stress, and to turn to drink.
Ex-England captain and Stoke manager Mick Mills released Mr Blackstock because at 5ft 4ins he was too small.
Mr Fox, now 58, had always strenuously denied the claims.
He told the court: "The gloving didn't go on."
Judge Phillip Butler ordered Mr Blackstock to pay £100,000 in costs to each of the defendants, which he must pay by 13 November.
He said: "I do not find the claimant's allegations are consciously dishonest or that nothing untoward ever occurred between players and apprentices at the club all those years ago, but I am unable to find as a fact that the specific events alleged by and allegedly involving the claimant did occur."
A statement released by Stoke City Football Club following the ruling said: "The club gives absolute reassurance that it is fully committed to the safety and protection of individuals at the club and has robust safeguarding policies in place which are frequently reviewed and updated."
Ex-Stoke City goalkeeper Peter Fox has been cleared of physically assaulting a trainee who claimed he was subjected to a ritual known as "gloving".