When grounded in methodological principles, historical within-case analysis can provide an effective approach to understanding historical processes and explaining complex issues across different fields. However, a review of domestic research practices indicates that its application in practice is accompanied by a number of challenges. This study seeks to identify these challenges through a purposive examination of 57 scholarly articles published in reputable domestic journals between 2015 and 2025. The articles were examined using thematic analysis. The findings indicate that a substantial proportion of the observed shortcomings stem from an incomplete understanding of the logic of within-case analysis, disruptions in the analytical architecture of the research, and the reduction of analysis to descriptive narrative. An interpretive examination of the relationships among these themes led to the formulation of an interpretive category termed “explanatory deficiency.” In this context, within-case analysis, which is fundamentally grounded in the construction of causal mechanisms within the specific context of a case, is reduced to a merely descriptive and narrative exercise that has limited consistency with the methodological foundations of the approach. The findings of this study can provide a basis for assessing and revisiting research design, the formulation of causal mechanisms, and the ways in which historical evidence is connected to causal explanation in historical within-case studies.