The resting metabolic rate (RMR) represents the largest component of total daily energy expenditure. The sale of ultra-processed foods (UPF) is increasing globally; however, UPF can have many adverse effects, including increasing inflammatory markers and altering RMRs. This cross-sectional study included 285 healthy overweight and obese women. Anthropometric measurements were evaluated using a bioelectrical impedance analyzer InBody 770 scanner. High-sensitivity C-reactive protein (hs-CRP), plasminogen activator-1 (PAI-1), monocyte chemoattractant protein (MCP-1), and interleukin-1 beta (IL-1β) blood levels were measured after a 12-h fasting. Indirect calorimetry was used to evaluate the RMR by using the Weir equation, and RMR deviation (RMR estimated - RMR actual), RMR per body mass index (BMI), and free fat mass (FFM) were estimated. A validated food frequency questionnaire (FFQ) was used, and seven groups of UPFs were extracted based on the NOVA method. A negative association between the RMR [β = −0.159, 95% confidence interval (CI): −0.471, −0.052, P = 0.044], RMR per BMI (β = −0.014, 95% CI: −0.025, −0.006, P = 0.036), and RMR per FFM (β = −0.241, 95% CI: −0.006, −0.000, P = 0.041) using the NOVA score was observed after adjusting for confounders. This association disappeared after inclusion of each inflammatory marker. All the markers may inversely mediate the relationship between the mentioned variables and the NOVA score. hs-CRP and MCP-1 also had a negative effect on the relationship between the NOVA score and RMR deviation. Finally, UPF intake is likely related with the RMR, mediated through changes in the production of hs-CRP, PAI-1, MCP-1, and IL-1β.