Duffy, 37, has joined the third-placed Championship side on a one-year contract after leaving Swinton Lions.
The Scotland assistant coach will lead Featherstone in their final league game against Toulouse on Saturday before the upcoming Super 8 Qualifiers.
"He is a fantastic coach and we are very excited to see how his reign here unfolds," chairman Mark Campbell said.
"We believe he has done a remarkable job in extremely difficult circumstances at Swinton and he deserves a great deal of credit for his efforts there."
Duffy, who played for Leigh, Widnes and Salford during a 16-year playing career, has been replaced by his former assistant Stuart Littler at fellow Championship side Swinton.
Featherstone Rovers have appointed John Duffy as head coach following the departure of Jon Sharp.