From there he would go on to direct the pilot and help with the creation of Space: Above and Beyond, Millennium, Sleepwalkers, Roswell, Dark Angel, Smallville, Tarzan, Without a Trace, Dr. Vegas, Jack & Bobby, Supernatural, Traveler, Terminator: The Sarah Connor Chronicles, The Mentalist, and Shameless.

Other directing highlights include "Join the Club", an Emmy-nominated episode of The Sopranos, and the 1998 feature film Disturbing Behavior.

In 2013, he directed the last two episodes of the third season: "The Rains of Castamere", which received the Hugo Award for Best Dramatic Presentation, Short Form,[5] and "Mhysa".

In 2015, he returned to the series Game of Thrones to direct the last two episodes of the fifth season, "The Dance of Dragons" and "Mother's Mercy".

In 2015, Nutter experienced a major injury that required several back surgeries, and had to skip directing any episodes of the next two seasons of Game of Thrones while he recovered.