Previous studies have shown that non-steroidal anti-inflammatory drug (NSAID) treatment in early lactation can have a positive impact on whole-lactation milk production in older cows. Our objective was to evaluate transcriptional changes in the mammary gland that could explain increased production responses. Sodium salicylate (SS; 125 g/d) or water (CON) were administered via oral drench to multiparous cows (n = 8/treatment) once daily for 3 d beginning approximately 24 h after parturition, and mammary tissue was collected on d 1, 4, and 45 postpartum. Day 1 tissue was collected immediately preceding the initial drench, and d 4 tissue was collected the day following the final drench. Total RNA extracted from tissue was deep sequenced and analyzed for differential gene expression using DESeq2. Only 16 of 18,286 genes were differentially expressed (false discovery rate <0.1) on d 45 due to NSAID treatment. Given the lack of milk yield and a low mammary transcriptome response to SS, additional analyses focused on time-dependent effects. Of the > 8500 genes that were differentially expressed (DE) over time, those meeting cutoff values of 1.5-fold change and adjusted p-value of <0.05 were used for functional analysis across time points in Ingenuity Pathway Analysis software. Analysis of transcriptional differences over time showed downregulation of pathways related to immune cell recruitment and differentiation, including cytokine signaling, TLR activation, inflammasome signaling, and interferon signaling, as well as cell growth and differentiation between wk 1 and 6 of lactation. STAT3 and PPAR signaling were upregulated on d 45 compared with the earlier time points. Additionally, DE genes in our data set showed extensive overlap with pathways related to cholesterol synthesis and retinoid X receptor signaling. Despite the low overall transcriptional effects of SS, transcriptome analysis emphasizes the extensive involvement of immune-related signaling pathways in the switch from lactogenesis to galactopoiesis.