The endocannabinoid system (ECS) controls feed intake and energy balance in nonruminants. Recent studies suggested that dietary management alters the expression of members of the ECS in the liver and endometrium of dairy cows. The aim of this study was to determine the relationship between body condition score (BCS) loss and the mRNA abundance of genes related to fatty acid metabolism and the ECS in the subcutaneous adipose tissue (AT) of dairy cows. The BCS was determined in multiparous (3.2 ± 0.5 lactations) Holstein cows at −21 and 42 days relative to calving (designated as d = 0). Cows were grouped into three categories according to BCS loss between both assessments as follows: (1) lost ≤0.25 unit (n = 8, low BCS loss (LBL)), (2) lost between 0.5 and 0.75 units (n = 8, moderate BCS loss (MBL)) and (3) lost ≥1 unit (n = 8, high BCS loss (HBL)). Concentrations of haptoglobin and non-esterified fatty acids (NEFAs) were determined in plasma. Real-time PCR was used to determine mRNA abundance of key genes related to fatty acid metabolism, inflammation and ECS in AT. Milk yield (kg/day) between week 2 and 6 post-calving was greater in the LBL group (49.4 ± 0.75) compared to MBL (47.9 ± 0.56) and HBL (47.4 ± 0.62) groups (P < 0.05). The overall mean plasma haptoglobin and NEFA concentrations were greater in MBL and HBL groups compared with the LBL group (P < 0.05). The mRNA abundance of TNF-α, Interleukin-6 (IL-6) and IL-1β was greatest at 21 and 42 days post-calving in HBL, intermediate in MBL and lowest in LBL groups, respectively. Cows in the HBL group had the greatest AT gene expression for carnitine palmitoyltransferase 1A, hormone sensitive lipase and adipose triglyceride lipase at 21 and 42 days post-calving (P < 0.05). Overall, mRNA abundance for very long chain acyl-CoA dehydrogenase and peroxisome proliferator-activated receptor gamma, which are related to NEFA oxidation, were greater in MBL and HBL groups compared to the LBL group at 42 days post-calving. However, mRNA abundance of fatty acid amide hydrolase was lower at 21 and 42 days post-calving in HBL cows than in LBL cows (P < 0.05). In summary, results showed a positive association between increased degree of BCS loss, inflammation and activation of the ECS network in AT of dairy cows. Findings suggest that the ECS might play an important role in fatty acid metabolism, development of inflammation and cow’s adaptation to onset of lactation.