Adverse maternal events around the time of conception influence embryonic development. Thus, aberrations in the uterine environment during early pregnancy, such as maternal metabolic or nutritional disruption, can alter gene expression in the developing embryo, leading to alteration in its developmental trajectory. Dietary supplementation of long-chain omega-3 polyunsaturated fatty acids (LCPUFA) improves metabolic and reproductive health across species. The objective of this study was to evaluate effects of peri-conceptual LCPUFA supplementation on endometrial and embryonic gene expression in overweight horses. Light horse mares (n = 13; mean age = 13.56 ± 0.11 yr; mean BCS = 7.07 ± 0.21) were supplemented with concentrate (n = 6) or an isocaloric, isonitrogenous diet containing 0.06 mg/kg BW marine-derived omega-3 LCPUFA (n = 7) 60 d before first sample collection. Four consecutive ovulatory cycles were monitored and uterine endometrial samples were obtained 12 d post-ovulation 1, 3 and 4. Mares were bred to one stallion on ovulatory cycles 2, 3 and 4, and embryos were flushed 12 d post ovulation. Candidate genes essential to inflammation, prostaglandin synthesis and embryonic development were evaluated by quantitative PCR. Data were log-transformed and analyzed using the GLM procedure in SAS (v9.3). When examining the data independent of breeding and pregnancy status, samples from LCPUFA supplemented mares contained reduced (P = 0.04) IL6 mRNA abundance and tended to have increased transcript abundance for Uterocalin (P = 0.09), SAA (P = 0.06) and IL10 (P = 0.06). Mares fed LCPUFA pregnant in cycle 3 contained greater IL10 (P < 0.001) and PLA2G3 mRNA (P = 0.009) and had a tendency for increased SAA abundance (P = 0.08). Supplemented mares bred but not pregnant in cycle 3 had a tendency for reduced expression of PTGER2 (P = 0.100). In the conceptus, relative transcript abundance of GATA4 and GATA6, markers of endoderm differentiation, along with GATA3 and ELF3, markers of trophectoderm differentiation were greater (P < 0.05) in embryos from LCPUFA supplemented mares (n = 5), than controls (n = 5). These results indicate that LCPUFA supplementation during the peri-conceptual period may alter the post-ovulatory uterine environment and early embryonic development in the horse.