Black had said he would review his position after coach Alberto Salazar was banned for four years by the United States Anti-Doping Agency.
Black will still oversee Sir Mo Farah's involvement in the Chicago Marathon as planned this weekend.
A statement from UK Athletics read: "UK Athletics have announced that Neil Black will leave his role as performance director at the end of October.
"Neil will commence a detailed handover with performance staff until his departure and will fulfil his role supporting Mo Farah at this weekend's Chicago marathon."
In 2015, when USADA began investigating potential doping violations, Salazar was coaching Farah. UK Athletics reviewed Salazar's link with Farah at the time and concluded there was "no reason to be concerned".
Black spoke about the matter on Monday after returning from the World Championships in Doha where Great Britain won just five medals, their worst performance since 2005.
He said: "I'll play back the decisions I made and once I've had a chance to really look through that I'll have a view."
Black, who has also described Salazar as a genius in the past, was appointed performance director following the resignation of Charles Van Commenee after missing medal targets at London 2012.
He previously worked with the governing body as a physiotherapist and as head of sport medicine and science. His involvement dates back to 1992.