Nicolay Nicolaysen was a founding member of the Society for the Preservation of Ancient Norwegian Monuments, of which he was president from 1851 to 1899. He also took active part in the restoration of the Nidaros Cathedral and of the Hall of Haakon IV (Håkonshallen). He was active in the founding the National Museum of Art, Architecture and Design (Nasjonalmuseet for kunst, arkitektur og design) and was a proponent of the Norwegian National Academy of Craft and Art Industry.
In 1852, the first investigations took place of the Borre mound cemetery (Norwegian: Borrehaugene from the Old Norse word haugr meaning mound) in Horten, Vestfold. Nicolaysen examined the excavations which uncovered an unusually good selection of craft work, of a form which as become known as Borre style, much of which is on display at the Viking Ship Museum in Oslo.
Excavations of the Munkeliv Abbey located at Nordnes in Bergen took place in 1857 and 1860. Many extremely well crafted structural fragments were recovered, now in the Museum of Cultural History (Kulturhistorisk Museum), part of Bergen Museum. These include the well-known marble head of Øystein Magnusson discovered by Nicolaysen, supposedly the oldest-known portrait of a Norwegian.
The first excavations of the Kaupang area was done in 1867. Nicolaysen mapped one of the grave-fields around the former town, and he excavated 79 grave mounds. Most archaeologists believe this was the first urban settlement of some significance in Norway.
Nicolay Nicolaysen is perhaps most known for excavating the Gokstad ship burial at Gokstad farm in Sandar, Sandefjord, Vestfold in 1880. Currently the ship, together with a burial chamber, two small boats and two tent boards from the burial chamber are displayed in the Viking Ship Museum in Oslo.
- Kunst og Haandverk fra Norges Fortid, Foreningen til norske (Fortidsmindesmærkers Bevaring, Kristiania 1881-1890)
- Mindesmærker af Middelalderens Kunst i Norge (1853–55)
- Norske Magasin. Skrifter og Optegnelser, angaaende Norge og forfattede efter Reformationen (1858–70)
- Norske Stiftelser. Samling af Fundatser, Testamenter og Gavebreve, samt historisk-statistiske Efterretninger vedkommende milde Stiftelser i Kongeriget Norge (1858–94)
- Absalon Pederssøn. Liber Capituli Bergensis (1860)
- Norske Bygninger fra Fortiden (1860–80)
- Norske Fornlevninger (1862–66)
- Om Throndhjems Domkirke (1872)
- Bergens Borgerbog 1550–1751 (1878)
- Om den gamle Bygningsskik i Solør og Østerdalen, i Folkevennen (1881)
- Langskibet fra Gokstad ved Sandefjord (1882)
- Om Relikviegjemmer i norske Kirker (1888)
- Stavanger Domkirke og de nærmest omliggende Bygninger (1896)
- Lidén, Hans-Emil, Nicolay Nicolaysen, Et blad av norsk kulturminneverns historie, Oslo 2005. ISBN 82-7935-187-6