The band announced on their Facebook page that the 52-year-old bassist has decided to leave the group.
The remaining members said in a statement they are "very proud" to have worked with Deal.
They disbanded in the early 1990s and reunited in 2004. Deal was also a part of the band The Breeders, which she formed and worked as lead singer and guitarist.
The Pixies' last tour was in 2011. Their last single was 2004's Bam Thwok.