The Menzies Remote Short-item Dietary Assessment Tool (MRSDAT) can be used to derive a dietary index score, which measures the degree of compliance with the Australian Dietary Guidelines. This study aimed to determine the relative validity of a dietary index score for children aged 6–24 months, living in a Remote Aboriginal Community (RAC), derived using MRSDAT. This validation study compared dietary index scores derived using MRSDAT with those derived from the average of three 24-h recalls. Participants were aged 6–36 months at the first dietary assessment and were living in a RAC. The level of agreement between the two methods was explored using Lin’s concordance correlation coefficient (CCC), Bland-Altman plots, weighted Cohen’s kappa, and Fischer’s exact and paired t-tests. Forty participants were recruited. The CCC was poor between methods (R = 0.35, 95% CI 0.06, 0.58), with MRSDAT estimating higher dietary intake scores for all food groups except fruit, and higher dietary quality scores by an average of 4.78 points/100. Community-based Aboriginal researchers were central to this validation study. MRSDAT was within the performance range of other short-item dietary assessment tools developed for young children, and shows promise for use with very young children in RACs.