Villarete started his engineering career in the academe, as a member of the faculty, 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 in Cebu City, Philippines. 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 Division, of SCHEMA Konsult, Inc. – Cebu Office. In 1999, he was also appointed as senior lecturer II at the University of the Philippines Visayas – Cebu College, Management Division, and taught Urban Planning subjects until 2010. 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. During his term in the Cebu City Government, former mayor Osmeña had particularly tasked Villarete with the city's two major projects: as project manager of the South Reclamation Project, and as project development officer of the Cebu City Bus Rapid Transit. He publicly stated his preference for Villarete to stay with the project. In September 2009, Nigel Paul Villarete was appointed by former Philippine President Gloria Macapagal Arroyo as a Member of the Board of Civil Engineering, Professional Regulation Commission, which is the official Philippine Government agency who gives the Licensure Examination for the professional practice of Civil Engineering, and to regulate the practice of the profession under the Civil Engineering Law.
Current appointment
Following his election as the fifteenth president of the Republic of the Philippines last May 10, 2010, President Benigno Aquino III has selected Nigel Paul C. Villarete to head the Mactan-Cebu International Airport. This move was supported by the Liberal Party in Cebu and by Cebu City's incumbent mayor, Michael L. Rama, who stated his support for Villarete, in response to Cebu Provincial Governor Gwendolyn Garcia who stated that the Presidential endorsement was not assurance for Villarete. He was selected by the MCIAA Board on October 20, 2010, and on October 26, 2010, Nigel Paul Villarete assumed office as the chief executive officer of the Mactan-Cebu International Airport Authority replacing Brigadier General Danilo Francia. The appointment was welcomed by Governor Gwen Garcia.