Police said in a statement that another 40 fans, who were not allowed to buy match tickets amid fears of hooliganism, have been sent home.
The Bulgarian authorities were warned this week by European soccer's governing body UEFA that hundreds of violent Dinamo fans, known as "Blue Bad Boys", were planning to travel to Sofia.
Ludogorets play Dinamo in a Group B match at the Vasil Levski national stadium, located in the centre of capital Sofia, because their 8,000-capacity Ludogorets Arena is not suitable for the Europa League's group stage matches.
Croatia's football association has been fined regularly in recent years for the bad behaviour of fans, who have chanted racist abuse and clashed with police at home and abroad.
Despite pledges by the authorities to curb the violence with stricter measures, little progress has been made.