It is a distance she can compete at without having to lower her testosterone levels after losing her appeal against the controversial rule change at the Court of Arbitration for Sport.
Under new IAAF rules, the double 800m Olympic champion can run in events from 400m to the mile by taking medication.
Semenya, 28, has said she will not take medication to comply and will run in Stanford, California on June 30.
The race will be her first since the rules came in on May 8, with Britain’s Laura Weightman also competing along with Sifan Hassan, Hellen Obiri and Genzebe Dibaba.
Prefontaine Classic meet director Tom Jordan said the request came from Semenya’s agent to race in the 3,000m.
“We were happy to oblige,” Jordan said, adding that he saw “no downside whatsoever.”
Semenya faces a tough challenge with a field packed full of talent.
She will be joined by world 5,000m champion Hellen Obiri, 2016 world indoor 1500m champion Sifan Hassan, and 2018 world indoor 1500m and 3,000m champion Genzebe Dibaba.