The suspect is 38-year-old Nima Momeni from Emeryville, California. Mr Lee and Mr Momeni knew each other, police said.
According to a LinkedIn profile for Mr Momeni, he is a technology consultant and start-up owner.
BBC reports Police found Mr Lee, 43, unconscious with stab wounds on 4 April near San Francisco's city centre.
He died in hospital from his injuries.
In a news conference on Thursday, San Francisco Police Department chief William Scott announced Mr Momeni's arrest.