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Joseph Stephen Flanagan, II, MD
Colon and Rectal Surgery, General Surgery
Male
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About me
Joseph Flanagan II, MD, is a colorectal surgeon with Atlantic Medical Group, specializing in disorders of the gastrointestinal tract that require surgical intervention. He is board-certified in surgery by the American Board of Surgery and fellowship-trained in colon and rectal surgery. He treats a wide range of gastrointestinal conditions including the surgical management of colorectal cancer, diverticulitis, inflammatory bowel disease, and benign and malignant anorectal disease.
Dr. Flanagan uses advanced techniques in colon and rectal surgery including robotics, laparoscopy, and open techniques tailored to each patient’s needs. He also performs colonoscopies (screening and diagnostic) and anorectal procedures. He takes the time to listen to his patients, answer their questions, and personalize each treatment plan to put his patients at ease.
After earning his medical degree from Rutgers New Jersey Medical School, Newark, Dr. Flanagan completed his residency training at Morristown Medical Center, where he was named chief surgery resident, responsible for running the surgical services including colorectal surgery, general surgery, surgical oncology, vascular surgery, and trauma surgery. He was selected to be the morbidity and mortality chief resident and education chief resident. He then completed a fellowship in colorectal surgery at Zucker School of Medicine at Hofstra/Northwell Health, Hempstead, NY.
Dr. Flanagan has published on several topics related to colon and rectal pathology in peer-reviewed medical journals. He is a participating provider of the Atlantic Accountable Care Organization.
SPECIALTIES
Colon and Rectal Surgery
General Surgery
AFFILIATIONS
Accountable Care Organization
Atlantic Medical Group
Chilton Medical Center
Morristown Medical Center
Where to see me
Education & Experience
TRAINING
Rutgers New Jersey Medical School
Medical School
Morristown Medical Center
Residency
Northwell Health
Fellowship
BOARD CERTIFICATIONS
Patient Reviews
4.9
- 5.0Apr 30, 2026Atlantic Health should have 10,000 doctors like Dr. Flanagan. His bedside manner, attention and knowledge is unlike any other doctor in the state of NJ. On a scale 1-10 he's a 15. Just amazing.
- 5.0Apr 16, 2026Dr. Flanagan was calming and put me at ease. He was very easy to talk to and he was excellent with providing details about the treatment he was providing.
- 5.0Mar 30, 2026I especially liked how Dr Flanagan drew a diagram to explain the situation
- 5.0Mar 27, 2026I truly could not have asked for a better experience overall! Everyone was pleasant, helpful, sympathetic, respectful. I was elated! Thank you.
- 5.0Mar 20, 2026Dr. Flanagan is one of the finest doctors I have come in contact with. His ability to treat with his clinical knowledge is rare these days. His knowledge, practical approach and EQ is commendable. I felt privileged to be treated by a doctor with great knowledge and clinical skills. Thank you Dr. Flanagan.
