Purpose: Innovations and best practices are the lifeblood of higher education institutions to make education is more student-centric and research-oriented. To make Higher Education Institutions (HEIs) more successful in achieving their objectives and to march towards excellency, it is desired to use their autonomy to improve the quality of education imparted by them by identifying and implementing in academics, administration, research and extension, and industry collaboration activities. In this paper, through an extensive review of literature, a research proposal in the form of a case study is developed systematically to identify and analyze various innovations & best practices in a higher education institution with special focus on academic, administrative, and research-related activities. Design/Methodology/Approach: A review-based research topic identification by collecting information from various published sources are analyzed using appropriate analysis frameworks as per exploratory research method. The research skills including design, analysis, comparison, evaluation, interpretation, and creation as proposed by Bloom’s Taxonomy for higher-level thinking are used while analyzing the collected information. Findings/Result: Based on review of literature using various keywords related to quality in higher education institutions, innovations and best practices in academics, administration, and research, the current status, desired status, research gap and research agendas are identified. By analysing the research agendas, the case study method of exploratory study on innovations and best practices in an autonomous University is selected for further research. The objectives of such case study and modality along with limitations are discussed. The procedure of carrying out such systematic research leading to PhD degree are proposed. Research limitations/implications: The research topic related to the research problem developed in this paper is one of the research agendas identified during the research gap analysis using the current status and desired status of the problem. The chosen topic for further research involves a case study on Innovations and best practices developed in academics, administration, and research & extension activities of a university. Depending on the autonomy and internal and external environments, the identified innovations and best practices can be generalized irrespective of the geographic region, culture, and tradition. Originality/New knowledge/Interpretation/Value: This article is focused on developing a new research project for proposed Ph.D. work. Based on a systematic review to know current status and desired status, the research gap, various research agendas to fill the gap, and a particular research agenda based on analysis are identified as research problem for a proposed case study research project. Further using the research problem, a research topic with the objectives and procedures are proposed as outcome. Paper Type: Review paper for research topic identification