UEFA says the 'racist behaviour' includes incidents targeting Romanian neighbor Hungary when the national team played to a 0-0 draw against Serbia on Sunday.
Romania fans also held up a banner linking refugees to terrorism, and a video posted on social media showed fans chanting a slogan supporting Serbia's territorial claim to Kosovo.
UEFA says its disciplinary panel will meet on October 25 to judge the charges, which include fans invading the field and lighting fireworks at the national stadium in Bucharest on October 14.
Sanctions could apply when Romania host Lithuania in the UEFA Nations League on November 17.