In 1852, he resigned his commission as a lieutenant with the Danish army, and earned his master's degree in sciences the following year.

As he grew older, he suffered from physical infirmities and during the last year of his life, he was stricken by paralysis.

[3] Lütken specialized in marine zoology, being highly regarded for his research of echinoderms.

[4][5][6] With Johannes Theodor Reinhardt (1816–1882), he published a book on Brazilian amphibians and reptiles titled Bidrag til Kundskab om Brasiliens Padder og Krybdyr.

[7] With Reinhardt, he described several herpetological species,[8] including the Little-scaled least gecko, the Rio Grande escuerzo and Saint Vincent's bush anole.