Instructional supervision is one of the important tasks for the principal of a school. The role of principal in the school is complex in nature; a role that involves many duties and responsibilities. One of the roles is being an instructional leader to help the teachers to improve their teaching. Improved teaching will automatically result in higher student achievement. The research aimed to compare instructional supervision in Army Public Schools & Colleges and Federal Government Educational Institutions in Pakistan. The significance of the topic lies in the worsening instructional quality in the schools which can significantly be improved by regulating the supervision process through principals who possess experience in both educational and administrative fields. The principal, an instructional leader, is the key figure in creating a school environment in which instructional leadership can thrive. The objectives of the study were; (a) to explore the instructional supervisory practices used in APS & Cs and FGEIs; (b) to find out the difference between perceived supervisory practices of instructional programs adopted by the heads of APS & Cs and FGEIs; (c) To evaluate the supervisory practices in APS & Cs and FGEIs in the light of existing supervisory practices; (d) to propose a model of supervisory practices for APS & Cs and FGEIs. The population of the study consisted of all the principals and secondary school teachers of APS & Cs and FGEIs in Pakistan. Mixed method research design was used; quantitative questionnaire and qualitative interviews were used to gather the data. For quantitative data 80 Heads of APS & Cs and 130 Heads of FGEI, 400 teachers from APS & Cs and 390 teachers from FGEIs were part of the sample through random sampling technique. Meanwhile, for qualitative data collection; 20 heads of the institutions from FGEIs and 10 heads of the institutions from APS & Cs, 20 teachers from FGEIs and 30 teachers from APS & Cs were selected for interviews through Purposive Sampling. Mean, standard deviation, and ttest were used as statistical tools for analysing data, whereas thematic analysis was used for qualitative data analysis. Acquired results from data were discussed while linking them with previous studies and theory. It was found that instructional supervision, its regularity, maintenance of record of supervision and its utility in the form of teachers’ punctuality, performance and improved instructional methodology based on feedback to the teachers is more frequent in APS & Cs than in FGEIs. The process needs to be further improved in FGEIs through effective measures taken at departmental level.