Dr. Flynn is an Associate Professor of Clinical Pediatrics at Weill Cornell Medicine and Associate Attending Pediatrician at NewYork-Presbyterian/Weill Cornell Medical Center. He has been a faculty member in the Weill Cornell Division of Pediatric Cardiology since 1993. 

In 2024, Dr. Flynn founded Avalon Pediatric Cardiology, a private practice affiliated with Weill Cornell on the Upper East Side, dedicated to expanding access to the outstanding Pediatric Cardiology care available at Weill Cornell and New York Presbyterian to a larger community of families. Dr. Flynn remains at Weill Cornell as a part-time faculty member, and continues to serve as Network Liaison for the Children's Heart Center of New York Presbyterian at Weill Cornell.

Dr. Flynn led the Pediatric Echocardiography Labratory from 2004 to 2024.  He served as Interim Co-Chief of the Division fom 2022 to 2024.

Dr. Flynn was named to the Castle Connolly List of Top Doctors in the New York Metropolitan Area for every year since 2008. He was selected by New York Magazine as one of New York's Top Doctors in every year since 2012.

Dr. Flynn has served Weill Cornell Medical College as Officer, Chair, and Senior Counselor of the General Faculty Council. He has also served as Officer and also President of the Pediatric Cardiology Society of Greater New York.

Dr. Flynn has participated in numerous international humanitarian medical missions aimed at performing and teaching the medical and surgical care of congenital heart disease in the developing world. These include: Healing the Children Guatemala Heart Mission, 1995; Surgeons of Hope mission to Fann Medical Center in Dakar, Senegal, 2007; Children's HeartLink missions to Jilin Heart Hospital in Changchun, China in 2008 and 2009, and the Post-Graduate Institute for Medical Education and Research in Chandigarh, India, in 2012. 

Dr. Flynn has been active in the teaching of medical students, residents and fellows throughout his career at Weill Cornell Medicine. He served as the Director of the General Pediatrics Residency Program from 1996-2000 and as Clerkship Director of the Pediatrics Subinternship from 1996-2008.

Dr. Flynn was elected to the Cornell chapter of the Alpha Omega Alpha Medical Honor Society in 1998. He has been elected by graduating medical students to the Senior List on three occasions. He received the Outstanding Teacher Award from the Pediatric Housestaff in 1996 and the Excellence in Teaching Award from Weill Cornell in 2000.

He graduated as class valedictorian from Villanova University in 1982, receiving the Leonardo da Vinci Award for excellence in science and the humanities. He received his medical degree from the University of Maryland School of Medicine. He completed his internship and residency at the New York Hospital-Cornell University Medical College, serving as Chief Resident in Pediatrics in 1989-90. His fellowship was performed in Pediatric Cardiology at the New York Hospital-Cornell University Medical College from 1990-1993.

Dr. Flynn is married to Dr. Shari Platt, Director of Pediatric Emergency Medicine at Weill Cornell. They have two sons who attended the The Town School, The Windward School, Trinity High School, IMG Academy, Cornell University and Wilmington University (Delaware). Dr. Flynn served on the Board of Trustees of the Town School from 2008-2014. He has served as the chair of the Parents Diversity Committee at Town and as Chair of the Board Diversity Committee. Dr. Flynn has been active in youth sports, coaching baseball and basketball with the Yorkville Youth Athletic Association and soccer with West Side Soccer League and New York Futsal.