Manchester United stars Paul Pogba and Marcus Rashford and Chelsea duo Tammy Abraham and Kurt Zouma are among those to have been targeted by trolls on the social media platform.
Accounts claiming to be fans of the clubs in question have directed abuse at the players after missed penalties and defensive mistakes, and others have also been targeted in recent weeks.
Twitter has insisted it is serious about the issue, which prompted former England striker Gary Lineker to join other celebrities and campaigners in pledging not to publicise the hateful comments they receive online.
Lineker said the abuse directed at the likes of England youngsters Rashford and Abraham was “frankly horrifying”, adding that work must be done to stop the sport “being tarnished in this way”.
Abraham, 21, said his mother was in tears after reading a torrent of racist comments targeted at him after he missed a decisive penalty in the European Super Cup against Liverpool last month.
Rashford, also 21, suffered a similar backlash after missing a spot kick against Crystal Palace in a league match.
Other footballers to have received abuse are Manchester City winger Raheem Sterling, who has regularly spoken out about the hateful comments he receives on social media, and West Ham midfielder Declan Rice.
Rice received threats from Republic of Ireland fans over his decision to switch his international allegiance to England, and was highly critical of the lack of action taken.
The Premier League, Football League and FA all attended a meeting with Twitter in London on Friday and said conversations were “positive and productive”.
In a joint statement, the three football bodies said: “The Premier League, EFL and FA today met Twitter with respect to the ongoing concerns surrounding discriminatory and hateful conduct taking place on the platform.
“The meeting was productive and positive, and gave both the football authorities and Twitter an opportunity to examine some of the specific issues around this unacceptable behaviour both online and offline.
“All parties agreed to take these constructive discussions forward.”
Sky Sports News understands football authorities also met with Facebook about the issue in the summer, and representatives from Twitter also spoke at a meeting of Football League clubs in Huddersfield last week.
The summit came after Manchester United and England defender Harry Maguire called on social media firms to verify accounts with passports so those responsible for abuse could be blocked and easily traced by police.
His words were backed by MPs including Damian Collins, chair of the digital, culture, media and sport committee.
Earlier this week, researchers at a US university claimed they have developed software that can identify cyber bullies and trolls on Twitter with 90% accuracy.
The team behind the machine learning tool said it could be used by social media platforms to help find and delete abusive accounts.