He is known for his works: Geronimo de los Reyes Building, Capitol Theater,Magsaysay Building, Captain Pepe Building, Philippine Village Hotel, Manila Jockey Club, Rufino Building, Rizal Theater, University of the Philippines Administration, and the reconstructed Rizal house in Calamba.
Some of his works:
The University of the Philippines-Diliman Administration Building

Quiapo Chruch was reconstructed in 1933 from plans by Nakpil.
Sources:
https://www.realliving.com.ph/lifestyle/arts-culture/architect-heroes-4-famous-buildings-by-juan-nakpil-a40-20160811
https://prabook.com/web/juan.nakpil/1288904
http://noypicollections.blogspot.com/2011/06/juan-f-nakpil-first-national-artist-for.html