John Tsoho of the Federal High Court in Abuja has stepped down from the trial of Nnamdi Kanu, leader of the Indigenous People of Biafra.
Mr. Tsoho is the second judge to do so.
Mr. Kanu is facing treason charges brought by the Nigerian government for leading a separatist group.
He has been in detention since October 2015. The first judge in the case, Ahmed Mohammed, stepped down in December 2015, after Mr. Kanu said he had no confidence in him.