Educated at the University of the Philippines with degrees in comparative literature and fine arts, he is acknowledged as the co-founder in 1976 of the UP Film Center where he served as its Assistant Director until 1990, spearheading the association called Chamber Film Group. He was a recipient of a John D. Rockefeller III Grant to study filmmaking at the New York University and film archiving at the Library of Congress Film Archives in Washington, DC and the Museum of Modern Art in New York. A British Council Grant led to further film studies and training in film archiving at the British Film Institute. Aguiluz had worked in various capacities in film projects with other important Filipino directors his senior, including National ArtistLino Brocka. He first made his mark with the 15-minute documentary Mt. Banahaw, Holy Mountain. The film won Silver Trophy at the prestigious Young Filmmakers of Asia Festival in Iran. Aguiluz plunged into the full-length feature in 1984 with the acclaimed Boatman. It was exhibited at the 1985 London Film Festival where it was cited as the outstanding film of the year. It was followed several years later, in 1995, by his own version of the story of the ill-fated household helper Flor Contemplacion in the equally acclaimed docu-drama entitled Bagong Bayani, OCW. In 1996, his film Segurista was picked as the official Philippine entry to the Oscars for the Best Foreign-Language Film category. It placed 12th in the list of thirty-nine titles. The same film won the Best Director award for Aguiluz at the Gawad Urian, as well as the Best Picture, Best Screenplay, Best Editing, Best Production Design and Best Supporting Actor plums, the last for actor Albert Martinez who played the title role. Segurista toured international film festivals in Toronto, Singapore and others. Aguiluz's next venture, Rizal sa Dapitan, was a historical film on the Philippine national hero's poignant exile in Dapitan. It captured the lion's share at the Philippine Movie Press Club's Star Awards and the Filipino Academy of Movie Arts and Sciences Annual Awards. The film was also shown at the First Philippine International Film Festival, at the Toronto International Film Festival, in Mar del Plata, Argentina and in Singapore. It continues its tour of world film capitals under the auspices of the Culture Committee of the UNESCO National Commission of the Philippines. When it competed at the Brussels International Film Festival, it was conferred the Grand Jury Prize in addition to the best actor award for lead star Martinez. Aguiluz has served on the jury of the film festivals in Berlin, Pusan, Singapore, Vesoul, Delhi, and Kerala in India, among others. He is the chief creative force behind the highly successful Cinemanila International Film Festival. In 2003, the French government awarded Aguiluz the Chevalier dans l'Ordre des Arts et des Lettres prize for his contributions to Philippine cinema. In 2013, the documentary film The Search for Weng Weng started its film festival run. In it Aguiluz was interviewed about the actor Weng Weng who was Philippines' first international star and a unique figure in cinema being a short person who performs death defying stunts. On January 8 2015, Aguiluz directorial effort Tragic Theater was released. The film is a supernatural horror film adaptation on the book of the same name, starring Andi Eigenmann, Christopher De Leon and John Estrada.
