Background/Objectives: The mainstay treatment of cow’s milk allergy (CMA) is to remove cow’s milk proteins from children’s dietary intake. In this context, dietary intake of children with CMA should be particularly checked and monitored. The objective of this study was to assess the applicability, usability, and accuracy of a new dietary intake (DI) assessment online tool (Nutricate© online application) for managing CMA in children. Subjects/Methods: This study used a pre-existing database of DI from the Nutricate© online application. DIs from 30 CMA children were used to compare micro/macronutrients (energy, protein, calcium, and iron intakes) calculated by Nutricate© and NutriLog© as the reference method. Comparisons were performed using the Pearson correlation analysis and the Bland–Altman plot. The Nutricate© tool usability was assessed via a System Usability Scale questionnaire (SUSq). Results: Correlation coefficient between the levels of micro/macronutrients obtained by Nutrilog© and Nutricate© software were highly significant (p = 0.0001) and were well-correlated (R coefficient > 0.6), indicating a very good concordance between the two methods. This observation was reinforced by the Bland–Altman plot, indicating the absence of proportional or fixed bias for energy, protein, calcium, and iron intakes. The mean SUSq score obtained was 81 ± 14, which is considered to be an excellent score. Conclusions: Nutricate© online application is a reliable method to assess micro/macronutrient (energy, protein, calcium, and iron intakes) intake in CMA children. Applicability and usability of this new dietary intake assessment online tool is excellent.