Vision Transformers (ViTs) have shown significant promise in computer vision applications. However, their performance in few-shot learning is limited by challenges in refining token-level interactions, struggling with limited training data, and developing a strong inductive bias. Existing methods often depend on inflexible token matching or basic similarity measures, which limit the effective incorporation of global context and localized feature refinement. To address these challenges, we propose Bi-Level Adaptive Token Refinement for Few-Shot Transformers (BATR-FST), a two-stage approach that progressively improves token representations and maintains a robust inductive bias for few-shot classification. During the pre-training phase, Masked Image Modeling (MIM) provides Vision Transformers (ViTs) with transferable patch-level representations by recreating masked image regions, providing a robust basis for subsequent adaptation. In the meta-fine-tuning phase, BATR-FST incorporates a Bi-Level Adaptive Token Refinement module that utilizes Token Clustering to capture localized interactions, Uncertainty-Aware Token Weighting to prioritize dependable features, and a Bi-Level Attention mechanism to balance intra-cluster and inter-cluster relationships, thereby facilitating thorough token refinement. Furthermore, Graph Token Propagation ensures semantic consistency between support and query instances, while a Class Separation Penalty preserves different class borders, enhancing discriminative capability. Extensive experiments on three benchmark few-shot datasets demonstrate that BATR-FST achieves superior results in both 1-shot and 5-shot scenarios and improves the few-shot classification via transformers.