Fishbone diagram, also called as ‘cause-and-effect’ diagram, is a tool used to identify the root cause of problems which represents the effect and the factors or causes influencing it. The tool is a template for brainstorming possible causes of an effect. As there could be infinite causes, this helps in identifying the root cause/s in a structured and precise way. An attempt has been made in this paper to use this technique to identify problems in the engineering education system in India, considering student and staff as the stakeholder. Major problems are classified and Fishbone diagram is used to analyse the root causes focusing on select parameters like personnel, academics, resources and universities. By identifying the causes, feasible solutions are suggested for improvement. A detailed analysis of student-staff problems is done by taking the case study of engineering institutes in general. The solutions suggested particularly are implemented in Sandip University Nashik.