Gerrard Scanlon, 53, from Enfield, north London, is accused of using threatening, abusive or insulting words likely to cause harassment, alarm or distress.
The delivery driver was released on police bail and is due to appear at Bromley Magistrates' Court on February 27.
He was arrested after Sky Sports News broadcast footage that appeared to show some of the London club's fans hurling insults at Senegalese striker El-Hadji Diouf during a game at the Den in November.
Millwall Football Club said it was "appalled" by the footage and vowed to reopen an investigation into allegations of racial abuse, which initially emerged online.
The club has promised to ban any individuals for life if they are found guilty, and captain Danny Shittu said he was "deeply saddened" by what he had seen in the documentary.
The footage appears to show fans hurling insults at Diouf during an npower Championship clash between the two clubs at the south-east London ground on November 18.
Shittu released a statement on Millwall's website which said: "I am deeply saddened by the documentary on Sky Sports showing racism by the minority at matches including at Millwall FC.
"As the current Millwall captain, racism is something I do not stand for or condone.
"I am currently in talks with the club about any further measures we can take in dealing with and eradicating racism at matches.
"I do not want the events shown yesterday to tarnish the hard work done by the club thus far and their efforts in tackling this issue."