Aims Shrub expansion is common in the tundra biome and has been linked to climate warming. However, the underlying mechanisms are still not fully understood. This study aimed to investigate the seasonal and vertical rooting patterns of different plant functional types, which is important for predicting tundra vegetation dynamics. Methods We harvested root samples by soil coring and investigated seasonal changes in root biomass and vertical root distribution across a vegetation gradient, focusing on the differences between graminoids and dwarf shrubs, at a northeastern Siberian tundra. Results Graminoid fine root biomass increased significantly during the growing season, whereas that of shrubs was already high at the beginning and did not change later on. Shrubs had a much shallower rooting pattern than graminoids. Also, shrub roots did not respond to increases in permafrost thawing depth over the growing season, whereas graminoids grew fine roots in deeper, recently thawed soil layers during the growing season. Conclusions Our results show that shrubs are predominantly shallow-rooted and grow roots earlier than graminoids, which allows shrubs to take advantage of the nutrient pulse after snowmelt in the early growing season. In contrast, the deep-rooted graminoids can access the nutrients in deeper soil and may profit from increasing permafrost thawing depth. The outcome of the competitive interactions between graminoids and shrubs in tundra may depend on the balance between the benefits associated with earlier root growth and deeper root distribution, respectively. The shrub expansion with climate warming observed in recent decades suggests that earlier root growth in the upper soil layer may be more important than increased rooting depth later in the growing season.