The 42-year-old will take over from RFU disciplinary manager Bruce Reece-Russel, who is retiring after 13 years in the post.
The RFU announced that McEvilly will join them in September, reporting to legal and governance director Karena Vleck and working in conjunction with RFU disciplinary officer His Honour Judge Jeff Blackett.
McEvilly is currently head of legal advice and hearings management with the General Pharmaceutical Council.
He joined the Hertfordshire RFU disciplinary committee in 2008 and in the same year started presenting cases for the RFU in rugby disciplinary and competition matters.
He was appointed last year to sit on the RFU disciplinary panel.
"I am delighted at being offered the role of head of discipline at the RFU and to be able to combine my regulatory and disciplinary experience with my passion for rugby," McEvilly said.