This is a place of genocide, the worst crime that can happen. It's hard to imagine that something like that can be done by a human being, Musharraf said in Potocari, where he laid flowers at the monument to the victims of the massacre.
He met women from Srebrenica and pledged Pakistan's assistance.
On Friday, Musharraf visited the northern town of Tuzla where he laid flowers at the monument commemorating Pakistani soldiers killed during service in the UN peace mission in Bosnia and Herzegovina.
In Sarajevo, he met behind closed doors with members of the Inter-Religious Council, which gathers religious officials from the Islamic, Christian and Jewish communities in Bosnia and Herzegovina.
Speaking to reporters after the meeting, the chairman of the Inter-Religious Council and head of the Islamic community, Mustafa Ceric, said that Musharraf had pleaded for compromise and reconciliation.