Abstract Background The mechanisms by which only some rheumatoid arthritis (RA) patients respond favorably to TNF blockade are still poorly characterized. The goal of this study was to identify biological features that explain this differential response using a multilevel transcriptome analysis of the synovial membrane. Methods Synovial samples from 11 patients on anti-TNF therapy were obtained by arthroscopy at baseline and week 20. Analysis of the synovial transcriptome was performed at the gene, pathway, and cell-type levels. Newly characterized pathogenic cell types in RA, peripheral helper T cells (T PH ), and CD34-THY1+ fibroblasts were estimated using a cell-type deconvolution approach. T PH association was validated using immunofluorescence. External validation was performed on an independent dataset. Results After multiple-test correction, 16 and 4 genes were differentially expressed at baseline and week 20, respectively. At the pathway level, 86 and 17 biological processes were significantly enriched at baseline and week 20, respectively. Longitudinal expression changes were associated with a drastic decrease of innate immune activity ( P  < 5e−30), and an activation of the bone and cartilage regeneration processes ( P  < 5e−10). Cell-type deconvolution revealed a significant association between low T PH cells at baseline and a better response ( P  = 0.026). Lower T PH cells were maintained in good responders up to week 20 ( P  = 0.032). Immunofluorescent analyses confirmed the accuracy of the cell-type estimation ( r 2  = 0.58, P  = 0.005) and an association with response. T PH association with anti-TNF response was validated in an independent sample of RA patients ( P  = 0.0040). Conclusions A lower abundance in the synovial membrane of the pathogenic T cell type newly associated with RA, peripheral helper T lymphocyte, is associated with a good response to anti-TNF therapy. Major changes in the myeloid cell compartment were also observed in response to therapy. The results of this study could help develop more effective therapies aimed at treating the pathogenic mechanisms in RA that are currently not well targeted by anti-TNF agents.