Trouble flared in the stands at Goodison during a heated second-half Europa League Group E clash with the French side on Thursday, October 19, last year.
It followed a melee involving players which moved towards supporters in the Gwladys Street end.
Today police confirmed three men have been charged with battery in connection with the ugly scenes.
Merseyside Police detectives investigated following a disturbance towards the front of the Lower Gwladys Street end and reviewed footage following the incident.
Today they said Michael Darren Fitzpatrick, 30, of Derby Square, Prescot; Callum McCready, 19, of Four Acre Lane, Clock Face, St Helens and Daniel John Helbert, 30, of Ashbourne Crescent, Roby have been charged with battery.
They are due to appear at Liverpool Magistrates’ Court on Wednesday, May 9.
Everton were hit with with a €30,000 fine following the crowd trouble during the game.
UEFA charged the club with “aggression by supporters against players”.
Television footage also showed one fan leaving his seat and appearing to hit out at a Lyon player, whilst also holding a child.