A recent study proposed a systematic “(budgeting) knowledge discovery educational framework” (BKDEF). This BKDEF is focused on guiding staff training courses for enhancing the ability to allocate the “large but limited” budget for single, high-cost product design. However, except for its initial application to support the budget planning for the next generation fighter design, the framework’s effectiveness is still awaiting further scrutiny. This study fills the gap by providing the “second application” of BKDEF, which is to support another similar decision for designing the medium-altitude long-endurance unmanned aerial system (MALE UAS). This paper verified the effectiveness of the framework through an empirical application and obtained the knowledge required to allocate a budget for MALE UAS design following the group-opinion basis. In addition, the original analytical style for the last “decision analysis” phase of BKDEF, which included pure quantitative analytical items in order to understand the similarities and diversities in the individual opinions, was replaced by a comparative study to discover the homogeneity and heterogeneity between the two budgeting decisions in a larger scope. As a consequence, the two criteria sets did not overlap despite both decisions being related to military aircraft design. The absolute weights for the MALE UAS design criteria were more balanced than those for the air-superior fighter design, even if the size of the criteria set was larger. The results pave a way for future studies on how other military aircrafts are designed, as more confidence about the use of a BKDEF can be gained from increasing applications, thus more insightful aerospace knowledge can be exploited in comparisons with these works.