Basal metabolic rate (BMR) measurement is time consuming and requires specialized equipment. Prediction equations allow clinicians and researchers to estimate BMR; however, their accuracy may vary across individuals with chronic spinal cord injury (SCI). The objective of this study was to investigate the validity of SCI-specific equations as well as able-bodied (AB) prediction equations in individuals with upper motor neuron (UMN), lower motor neuron (LMN), and females with SCI. Twenty-six men and women with chronic SCI (n = 12 innervated males, n = 6 innervated females, n = 8 denervated males) participated in this cross-sectional study. BMR values were measured by indirect calorimetry. Body composition (dual-energy X-ray absorptiometry and anthropometrics) assessment was conducted. AB-prediction equations [Cunningham, Nelson, Owen, Harris and Benedict, Mifflin, Schofield, Henry] and SCI-specific equations [Chun and Nightingale & Gorgey] were used to estimate and validate BMR. The accuracy of AB-specific FFM equations in predicting BMR was evaluated using Bland-Altman plots, paired t-tests, and error metrics. Measured BMR for innervated males, females, and denervated males was 1436 ± 213 kcal/day, 1290 ± 114, and 1597 ± 333 kcal/day, respectively. SCI-specific equations by Chun et al., Nightingale & Gorgey, and AB-specific FFM equations accurately predicted BMR for innervated males. For the denervated males, Model 4 equation by Nightingale & Gorgey was not different (p = 0.18), and Bland-Altman analyses showed negative mean bias but similar limits of agreement between measured and predicted BMR for the SCI-specific equations and AB-specific FFM equations. We demonstrated that SCI-specific equations accurately predicted BMR for innervated males but underpredicted it for denervated males. The Model 4 equation by Nightingale & Gorgey accurately estimated BMR in females with SCI. Findings from the current study will help to determine caloric needs in different sub-groups of SCI.