Kuenne was born October 24, 1973 in Mountain View, California He grew up in Northern California, and began making films aged seven on Super 8 film and later video. He studied film at University of Southern California's School of Cinema-Television, where he made Remembrances (1995) and was awarded the Harold Lloyd Scholarship in Film Editing. Kuenne then studied film composing, but returned to directing with feature Scrapbook (1999). In 2002 he was awarded an Academy of Motion Picture Arts and Sciences Nicholl Fellowship in Screenwriting for a script titled Mason Mule.
Validation (2007), written, directed, and scored by Kuenne, was distributed through Gay Hendricks's Spiritual Cinema Circle and is a short film about a parking attendant (played by T. J. Thyne) who dispenses compliments to his customers. It won Best Short Grand Prize at the 2007 Heartland Film Festival, and The Independent Critic rated it A+. It has received more than 9 million YouTube views.
Kuenne's documentary Dear Zachary (2008), about the murder of his childhood friend Andrew Bagby, was received as a documentary that "will rip you apart inside and pour your guts out through your tear ducts".
His latest feature film Shuffle (2011) again stars T. J. Thyne, playing a man who finds his life running out of sequence. It won the Jury Award for Best Feature at the 17th Stony Brook Film Festival.