Abstract Post-infectious Lyme arthritis (LA) is a model for testing the causal relationship between infection and autoimmunity. The initial trigger for LA, Borrelia burgdorferi infection, is known with certainty, but it is unclear why some patients have persistent synovitis after completion of antibiotic therapy. To elucidate the inflammatory nature of post-infectious LA, whole transcriptome sequencing was performed on synovial tissue from 14 patients with post-infectious LA and compared with that from patients with other forms of inflammatory arthritis or degenerative arthritis. LA patient synovial tissue had a highly inflammatory expression signature, similar to patients with other immune disorders including Type IV hypersensitivity and autoimmune diseases. This profile included upregulation of IFN-responsive genes and genes associated with MHC Class II antigen processing and presentation, T cell activation, and cell-mediated cytotoxicity; and down-regulation of genes involved in tissue repair and cell metabolism. Fibroblasts isolated from synovial tissue and primary fibroblasts in vitro expressed markers of inflammation and active proliferation, consistent with the tumor-like proliferative nature of the synovial lesion. miR-155, a proinflammatory and oncogenic microRNA, was highly expressed and positively correlated with markers of inflammation and Class II antigen presentation. Expression of tumor suppressor let-7a was downregulated, negatively correlated with markers of inflammation, and positively correlated with markers of appropriate wound repair. We postulate that these two microRNAs potentiate epigenetic transformation of synovial fibroblasts into an auto-inflammatory and proliferative phenotype.