Objective The causes of protein malnutrition and body composition changes in chronic kidney disease (CKD) are poorly understood. Alterations to metabolic rate caused by CKD may be a contributor. Using the doubly labeled water technique and indirect calorimetry, we set out to determine whether reduced glomerular filtration rate is associated with alterations to total energy expenditure (TEE) and resting energy expenditure (REE). We also aimed to determine whether TEE in patients with CKD can be easily predicted from a physical activity questionnaire. Methods In a prospective, observational study we evaluated 80 patients (52 men; mean age 56.7 ± 16.2 years) with CKD ranging from stage 1 to stage 5 with estimated glomerular filtration rate (eGFR) calculated by the Chronic Kidney Disease Epidemiology Collaboration equation (CKD-EPI). TEE was measured using doubly labeled water isotope excretion over 14 days (TEEDLW), REE by indirect calorimetry (REEIndirectCal) and physical activity level using the Stanford 7-day recall questionnaire. Results eGFR did not correlate with TEEDLW and REEIndirectCal. Findings with weight-adjusted energy measures were similar. REEIndirectCal and TEEDLW were significantly lower in patients whose eGFR was <50 mL/min/1.73 m2 and those with higher levels. There were similar findings with respect to weight-adjusted energy measures. In multivariable analysis, age, sex, and weight were independent predictors of TEEDLW and REEIndirectCal. eGFR did not predict TEE or REE in either of these models. Conclusion There was no direct relationship between reduced renal function and metabolic rate. Differences in energy metabolism at lower levels of glomerular filtration rate are more likely to be due to factors such as age, body composition, and physical activity.