High-latitude tundra ecosystems are increasingly affected by climate warming. As an important fraction of soil microorganisms, fungi play essential roles in carbon (C) degradation, especially the old, chemically recalcitrant C. However, it remains obscure how fungi respond to climate warming and whether fungi, in turn, affect C stability of tundra. In a two-year winter soil warming experiment of 2 °C by snow fences, we investigated responses of fungal communities to warming in the active layer of the Alaskan tundra. Although fungal community composition, revealed by 28S rRNA gene amplicon sequencing, remained unchanged (P > 0.05), fungal functional gene composition, revealed by a microarray named GeoChip, was altered (P < 0.05). Changes in functional gene composition were linked to winter soil temperature, thaw depth, soil moisture, and gross primary productivity (Canonical Correlation Analysis, P < 0.05). Specifically, relative abundances of fungal genes encoding invertase, xylose reductase, and vanillin dehydrogenase significantly increased (P < 0.05), indicating higher C degradation capacities of fungal communities under warming. Accordingly, we detected changes of fungal gene networks under warming, including higher average path distance, lower average clustering coefficient, and lower percentage of negative links, indicating that warming potentially changed fungal interactions. Together, our study revealed higher C degradation capacities of fungal communities under short-term warming and highlights the potential impacts of fungal communities on mediating tundra ecosystem respiration, and consequently future C stability of high-latitude tundra.