Micro-expression recognition is one of the most challenging topics in affective computing. It aims to recognize tiny facial movements difficult for humans to perceive in a brief period, i.e., 0.25 to 0.5 seconds. Recent advances in pre-training deep Bidirectional Transformers (BERT) have significantly improved self-supervised learning tasks in computer vision. However, the standard BERT in vision problems is designed to learn only from full images or videos, and the architecture cannot accurately detect details of facial micro-expressions. This paper presents Micron-BERT (µ-BERT), a novel approach to facial micro-expression recognition. The proposed method can automatically capture these movements in an unsupervised manner based on two key ideas. First, we employ Diagonal Micro-Attention (DMA) to detect tiny differences between two frames. Second, we introduce a new Patch of Interest (PoI) module to localize and highlight micro-expression interest regions and simultaneously reduce noisy backgrounds and distractions. By incorporating these components into an end-to-end deep network, the proposed µ-BERT significantly outperforms all previous work in various micro-expression tasks. µ-BERT can be trained on a large-scale unlabeled dataset, i.e., up to 8 million images, and achieves high accuracy on new unseen facial micro-expression datasets. Empirical experiments show µ-BERT consistently outperforms state-of-the-art performance on four micro-expression benchmarks, including SAMM, CASME II, SMIC, and CASME3, by significant margins. Code will be available at https://github.com/uark-cviu/Micron-BERT