This study investigates structural influence of the Madrassah system on effectiveness of its students in terms of civic health, system thinking and professional development. The researchers constructed the instrument of survey after rigorous literature review, frequent interaction with scholars, clerics and policy makers. The survey was administrated to 600 Madrassah’s students from different schools of thought. By applying T-test and Kruskal Waliss Rank Test for measurement of effectiveness and Structural Equation Modeling methodology the researchers has explored the relationship between the (...) variables, and later analyzed with the help of selected model. Findings of the study demonstrate that education system followed in Madrassahs does not seem to be effective and need-based in contemporary times. Indicators of Madrassah structure such as curriculum and openness negatively influences the students while peda­gogy positively influences the effectiveness of students of Madrasah in Pakistan. In the end, it is recommended that curriculum and pedagogy of Madrassah should be reformed and updated in accordance with knowledge-based economy. This will not only upgrade the poor segment of society but also bring together the variety of individuals close enough to understand each other. (shrink)