To solve the problem of comparative efficiency analysis of branch operations for a small volume of randomly observed data, a non-parametric approach is relevant, since it does not require a probabilistic model of observations. Comparing the results of the non-parametric approach with the results obtained within the traditionally used Gaussian model is also relevant. Additionally, obtaining a consistent comparison of a group (of no less than three) branches is important. Currently, the non-parametric approach and the corresponding comparison with the known results of solving the problem considered in this work obtained within the framework of the normal model are absent. In addition, insufficient attention is paid to the search for methods of obtaining consistent solutions. This work to some extent fills these gaps. This work uses non-parametric statistical methods and theory of simultaneous hypothesis testing to address these problems. This paper proposes a procedure for comparative analysis of the efficiency of several units within a network organization with a small volume of observations based on the Mann–Whitney tests. We carry out a comparison of the results obtained from the proposed non-parametric procedure with results based on extensions of Student’s t-tests. We propose a method for reducing the number of compatibility problems based on the search for an appropriate significance level. We provide an example of a fully consistent comparison of the efficiency of branch operations.