This year's competition was only held for the short film category. The winners are:
- Best Screenplay: Papetir
- Audience Choice: Sanctissima
- Best Film: Pusong Bato (Stone Heart)
- Best Direction: Lisyun Qng Geografia (Geography Lessons)
- NETPAC Prize: Wawa
- Special Jury Prize: Wawa
- Apasol (Chasing Sun) by Ryanne Murcia
- Gatilyo ng Baril by Glenmark Doromal and Eero Yves Francisco
- Kyel by Arvin Belarmino
- Lisyun Qng Geografia (Geography Lessons) by Petersen Vargas
- Mater by Annemikami Pablo
- Nenok by Milo Tolentino
- Papetir by Darwin Novicio
- Pusong Bato (Stone Heart) by Martika Ramirez Escobar
- Sanctissima by Kenneth Dagatan
- Wawa by Anj Macalanda
The finalists for the Full-Length Feature category for Cinemalaya 2016 were also announced at the event. These finalists will receive production grants of P700,000 each. The winner of the best film for this category will also receive P250,000. The finalists for Full-Length Feature are:
- Ang Bagong Pamilya Ni Ponching by Inna Salazar and Victor Villanueva
- Ang Mga Bisita ni Mamang by Janice O'Hara and Denise O'Hara
- Dagsin by Atom Magadia
- Hiblang Abo by Ralston Jover
- I America by Ivan Andrew Payawal
- Kusina by David Corpuz and
- Lando at Bugoy by Vic Acedillo, Jr
- Mercury is Mine by Jason Paul Laxamana
- Pamilya Ordinaryo by Eduardo Roy, Jr
- Tuos by Derick Cabrido