Tumor necrosis factor receptor-associated factor-2 and Nck-interacting protein kinase (TNIK), which is a member of the germinal center kinase (GCK) family, represents a potentially crucial target for tumors, fibrosis, inflammation, and neurological diseases. This is due to its role in regulating significant signaling pathways, including Wnt/β-catenin, TGF-β, Merlin and FAK signaling, as well as the PI3K, AKT, and mTOR pathways. To date, numerous TNIK inhibitors with diverse structures and high in vitro enzyme inhibitory activities have been reported. However, their subsequent development has been hindered by issues such as low selectivity, high toxicity, and suboptimal in vivo therapeutic efficacy. This paper aims to comprehensively review the latest progress in the structural characteristics and pharmacological effects of small-molecule TNIK inhibitors. By doing so, it seeks to offer valuable insights and guidance for the future development of more effective TNIK inhibitors.