PipeTransformer leverages automated elastic pipelining for efficient distributed training of Transformer models. In PipeTransformer, we designed an adaptive on-the-fly freeze algorithm that can identify and freeze some layers gradually during training and an elastic pipelining system that can dynamically allocate resources to train the remaining active layers. More specifically, PipeTransformer automatically excludes frozen layers from the pipeline, packs active layers into fewer GPUs, and forks more replicas to increase data-parallel width. We evaluate PipeTransformer using Vision Transformer (ViT) on ImageNet and BERT on SQuAD and GLUE datasets. Our results show that compared to the state-of-the-art baseline, PipeTransformer attains up to 2.83-fold speedup without losing accuracy. We also provide various performance analyses for a more comprehensive understanding of our algorithmic and system-wise design.