(1) Background: Microbiological assay of active medicinal compounds is superior to conventional chemical means in several circumstances to date. However, ensuring the validity and suitability of the assay design proposed for the intended purpose is crucial before deriving any records or conclusions from the results of the potency determination; (2) The present work represented statistical comparison between three design models for determination of the potency of Neomycin Sulfate antibiotic using agar diffusion technique for the same test material subject under identical conditions through the application of a combination of statistical software programs, including validated programmed Microsoft Excel Workbook for the statistical testing of each assay layout; (3) Results: raw data of the three assay designs were found to be reasonably valid for further analysis of the assay suitability. Examination of the sources of variations for each design demonstrated the validity of the conducted experimentation. Variation between the computed potencies from the three designs was lower than 5 µg/mg. However, there was significant variation between the confidence windows of each type; (4) Conclusions: 2 x 4 design had the narrowest confidence range. However, improving confidence would require investigation of the assay parameters, including the modification of the number of replicates per treatment.