Roy will succeed Lesley-Anne Knight, who served as the charity's secretary-general from 2007-2011. She was denied the possibility of seeking election for another term.
Roy is currently the international lobbying and advocacy director for Secours Catholique (Caritas France). He has worked for the French charity for 30 years.
He has worked on global governance, improving development financing, promoting peace and lobbying extractive industries through membership of the Extractive Industries Transparency Initiative (EITI) Governing Board and Coordinator of the French "Publish what you pay" platform.
Speaking to the assembly in Rome immediately after the vote, Roy said he was "very moved" by his election. "I'd like to thank Lesley-Anne for the work she's done so far, and also all of you for the work that you do for this network which reflects the hopes of the poor to build a better world," he added.
Roy will serve as secretary-general alongside Cardinal Oscar Rodríguez Maradiaga, the archbishop of Tegucigalpa, Honduras, who was re-elected for a second term as Caritas Internationalis president this week.
Caritas members are in Rome through Friday for the 19th general assembly of the confederation of diocesan charitable organizations from around the world. This year's assembly marks the 60th anniversary of the confederation, which joins some 165 Catholic charity organizations.