The present study aimed to contribute to the knowledge of the diversity of Timor’s pteridophytes and lycophytes, with particular emphasis on Timor-Leste. Drawing on extensive fieldwork across much of Timor-Leste’s territory, together with the study of herbarium specimens and the literature, we compiled a database of almost 1,200 specimens, resulting in a checklist of 215 taxa. Of these, 52 represent, to the best of our knowledge, new records in the literature for Timor, while 31 misapplied names were corrected. The new fieldwork contributed with 315 (27%) additional herbarium specimens, adding to the 124 (10%) collected by Paiva, Silveira and Sousa in 2004 and 2005, all of which will be deposited in the collections of the Herbarium of the University of Aveiro (AVE), the Herbarium of the Naturalis Biodiversity Center, Leiden (L), and the future Herbarium of the University of Timor Lorosa’e. The next three most abundant collections were the 144 (12%) made by Ruma in West Timor, the 84 (7%) made by H.O. Forbes, and the 81 (7%) made by I. Cowie and colleagues of the Northern Territory Herbarium, Australia (DNA), both in Timor-Leste. Extinction risk was assessed at the global level for three endemic species, and at the regional level, for the island of Timor, for six forest species: one was assessed as CR, three as EN, three as VU, one as LC and one as DD. Future studies should extend collection efforts to the many unexplored areas of Timor, ideally gathering demographic and threat-related information to assess the conservation status of the remaining species, especially the rarer and endemic ones.