The Republic of Ireland forward was at home on international duty last June when the alleged incident took place in a Dublin bar
The Republic of Ireland international has been released on bail and will appear before the Dublin District Court on May 29.
Stokes was arrested by Irish police in August 2013 before being questioned and released without charge. A file was then sent to the Director of Public Prosecutions who decided to prosecute.
Stokes was arrested by arrangement on Chancery Street in Dublin on Thursday afternoon. He was charged under section three of the Non-Fatal Offences Against the Person Act 1997 with assault causing harm.
The incident allegedly took place on June 8 2013 following a World Cup 2014 qualification match between Ireland and the Faroe Islands at the Aviva Stadium.