He will remain in the third tier following Rotherham’s relegation, which led to the sacking of Evans’ predecessor Leam Richardson.
Rafferty told BBC Radio Solent last week that he “totally disagreed” with Portsmouth boss John Mousinho’s decision about his future.
“I felt like I was the right person for the job next season in the role but he explained that it was something slightly different he wanted,” he said.
“It was a disappointment and a bit of a shock but that’s football – I had something in the back of my mind preparing me for it.”
