Dr. Allen is also the co-founder and co-director of the Center for Prisoner Health and Human Rights at Brown University.

Dr. Allen began his work in health and human rights at the age of 17 in Cambodian refugee camps in Thailand, listening to the stories of those who had escaped the Khmer Rouge torture and killing fields. After returning to the United States to complete his medical studies, he embarked on a career of caring for underserved and marginalized populations. Following three years in the National Health Services Corps in the Mississippi Delta and Rhode Island, he served for seven years as a full-time physician for the Rhode Island Department of Corrections, acting as the department medical program director between 2001 and 2004. During that period, he published the first report of successfully treating hepatitis C in a prison setting, a paper that helped secure access to treatment for incarcerated patients across the nation. In 2004, Scott left that position and joined Physicians for Human Rights as a Columbia University Medicine as a Profession Fellow in its investigations into the treatment of Iraqi prisoners at Abu Ghraib and the examination of the Bush Administration interrogation program particularly of the participation of health professionals.

In 2011, he joined the newly formed medical school at UCR as one of the founding full-time clinical faculty. He would go on the serve as Associate Dean of Academic Affairs, Chair of the Department, and briefly as Chair of the Clinical Division.

In 2018, in the course of work done as a medical experts for the Office of Civil Rights and Civil Liberties in the Department of Homeland Security, Dr. Allen and his colleague Dr. Pamela McPherson became whistleblowers when they made protected disclosures to congress about the harms of family detention in the U.S. immigration. He subsequently sounded the alarm, along with Center Director Dr. Jody Rich, about the threat of COVID-19 to detention and correctional facilities.

As practicing clinicians, Dr. Allen and his wife Dr. Emma Simmons founded and see patients at the Access Clinic, a primary care clinic in Southern California for adults with developmental disabilities.