The court said Sylvestre Mudacumura, the leader of the Democratic Forces for the Liberation of Rwanda (FDLR), was wanted for nine war crimes.
A fresh warrant was also served for renegade soldier Bosco Ntaganda, adding charges to those he already faces.
Both men are accused of targeting civilians in the east of the country.
Former ICC prosecutor Luis Moreno-Ocampo previously described the men as "the most dangerous" operating in the region.
In a written decision, judges said there was information to suggest that Maj-Gen Mudacumura, a Rwandan Hutu leader based in DR Congo, committed nine war crimes, including murder, mutilation, rape and pillage.
The charges date to conflict in North and South Kivu in 2009-2010.
Maj-Gen Mudacumura is the field commander of the FDLR whose leaders are believed to have taken part in the 1994 genocide in Rwanda.
Its members include extremist Hutus, who took cover in neighbouring DR Congo after the end of the mass killings which claimed the lives of some 800,000 people, mostly ethnic Tutsis.
Both Kinshasa and Kigali - which accuses DR Congo of sheltering the rebel leader - welcomed the court's move. Rwanda's justice minister told AFP news agency that it was "better late than never".
The ICC had previously turned down a request for a warrant against Maj-Gen Mudacumura.