Leonen was dean of the University of the Philippines College of Law from 2008 to 2011. He is well known in the fields of environmental activism and community organizing.
After finishing high school at Saint Louis University-Boys' High School as valedictorian, Leonen graduated magna cum laude with a degree in economics from the University of the Philippines in 1983 and served as chairman of the organization Economics Toward Consciousness, a student organization based in the University of the Philippines School of Economics, in A.Y. 1982-1983. He obtained his law degree from the university's College of Law in 1987. Later that year, he co-founded the Legal Rights and Natural Resources Center, Inc.-Kasama sa Kalikasan, a legal and policy research and advocacy institution which focused on providing legal services for upland rural poor and indigenous people's communities. He served as the Center's executive director for fifteen years. He then left for Columbia University in New York, USA for his Master of Laws degree.
Leonen joined the law faculty in 1989 as professorial lecturer in Philippine Indigenous Law. He became assistant professor during the term of Dean Pacifico Agabin and started to do work as an academic administrator under the term of Dean Merlin M. Magallona. In 2000, he joined the UP System administration as University General Counsel. In March 2005, he became the first Vice President for Legal Affairs of the University of the Philippines. Leonen has taught 20 different subjects in the law school. He also served as director of the clinical legal education program of the college. His teaching competence is not only acknowledged in the CL but also in other institutions like Miriam College and the Philippine Judicial Academy, to cite a few. He has extensively lectured and acted as resource speaker in other national and international fora such as those conducted in Hong Kong, Thailand, Malaysia, Indonesia, Japan, Spain, Netherlands, Australia, Estonia and the United Kingdom.
In 2008, he was selected as the Dean of the University of the Philippines College of Law by the Board of Regents of the University of the Philippines. He served as Dean until the appointment of incumbent Dean Danilo L. Concepcion in June 2011.
Leonen has also provided legal commentary for television networks such as ABS-CBN and GMA Network during the coverage of such events as the 2001 impeachment trial of President Joseph Estrada.
In July 2010, Leonen was named by Philippine President Benigno Aquino III as the Philippine government's chief negotiator with the Moro Islamic Liberation Front. Under his leadership, the government successfully sealed a framework agreement with the MILF for the establishment of the Bangsamoro political entity to replace the Autonomous Region for Muslim Mindanao. His performance was hailed by different sectors in society, bringing new hopes for an everlasting peace in the war-torn Mindanao.
On 21 November 2012, President Benigno Aquino III named Leonen as the 172nd Associate Justice of the Philippine Supreme Court at the age of 49. Leonen will be the youngest Justice in the current century after incumbent Chief Justice Sereno.
In oral arguments, Leonen frequently challenges the arguer's position with his stringent lines of questioning. He has a remarkable command of the Socratic method in order to test positions and arguments of counsel appearing in Court.
In a landmark case of Belgica v Executive Secretary, where the Court declared the Pork Barrel System unconstitutional, Leonen wrote a separate concurring opinion where he displayed great command of logic and the law in order to arrive with conclusions regarding the unconstitutionality of pork barrel. He said, "A member of the House of Representatives or a Senator is not an automated teller machine from which the public can withdraw funds for sundry private purposes."