Villarete started his engineering career as a member of the faculty of the Civil Engineering Department of the Cebu Institute of Technology in 1983. In 1986, he was appointed as the head of the Civil Engineering Department, College of Engineering and Architecture, of the University of the Visayas (UV) in Cebu City, Philippines.^{[citation needed]}

In 1989, he was appointed as monitoring and evaluation engineer of the Province of Cebu, and later was appointed as chief of infrastructure of NEDA Reg. 7, a post he held until 1994. In 1995, Villarete then became the manager for Planning, Studies, and Development (PSAD) Division, of SCHEMA Konsult, Inc. (SKI) – Cebu Office. In 1999, he was also appointed as senior lecturer II at the University of the Philippines Visayas – Cebu College (UPVCC), Management Division, and taught Urban Planning subjects until 2010.^{[citation needed]}

In 2001, then Mayor Tomas Osmeña appointed Villarete as city administrator of Cebu City. After two years, Osmeña appointed Villarete as city planning and development coordinator, a position he held until October 25, 2010, when he was appointed as general manager of the Mactan–Cebu International Airport, CEO of MCIAA. While Villarete was nominated by President Benigno Aquino III on May 10, 2010,^[4][5][6] he was not selected by the MCIAA Board until October 20, 2010,^[7] and on October 26, 2010, he assumed office as the chief executive officer of the Mactan–Cebu International Airport Authority (MCIAA)^[8] replacing Brigadier General Danilo Francia (Ret.).

As of 2019, Villarete was again serving as Cebu City administrator during which time he served on the mayoral transition team.^[9][10]