During his first years of practice, Arruda worked at the Public Health Department in Laval. From 1998 to 2012, he was an assistant clinical professor in the Department of Social and Preventive Medicine at the Université de Montréal. He was director of public health protection at the Quebec Ministry of Health and Social Services from 2000 to 2012. In May 2012, he was appointed National Director of Public Health. While working for this ministry, he has been involved in the management of the SARS outbreak in 2003, the H1N1 pandemic in 2009, and in public health measures during the Lac-Mégantic rail disaster in 2013.