Ferns and lycophytes are excellent model organisms to investigate the effect of climate change on species niches, due to their high sensitivity to changes in temperature and precipitation. In Honduras, this species group is particularly diverse with over 713 known taxa. However, we currently lack a quantitative assessment of the impact that changes in climate might have on these species. This study aimed (1) to explore the structure of the available climatic conditions across the entire country; (2) to determine the extent to which the available climatic space is occupied by different fern and lycophyte species; and (3) to assess which regions of climatic space will be most affected according to scenarios of climate change. We analyzed a newly developed database of herbarium fern records (n = 11,791) and used ordination models to compare the climatic niche of all Honduran fern and lycophyte taxa under present and future climates. We found that species were distributed throughout most of the available climatic space. Under RCP2.6 and RCP8.5 projections 128 to 391 species will have their average niche positions outside of the predicted available climatic space by the years 2049–2099. Particularly affected will be species that grow in low temperature and high precipitation areas, which represent high altitude parks, such as Celaque National Park. Epiphytes showed smaller variance in their climatic niches than terrestrial species. However, terrestrial species showed higher loss in climate space (e.g., 82.9% vs. 17.1% for RCP8.5) and are more likely to be at risk in the future. In general, Honduras is expected to become drier, with more extreme events of severe drought. Considering that ferns are particularly sensitive to changes in climate, if tested in the future, they could be used as a proxy for other Honduran plant taxa.