In recent time, most Nigerian public universities find it very difficult to manage the meagre resources available to them and this has hampered effective delivery of services that are germane to achieving rapid development in terms of infrastructure, training and re-training of teaching and administrative personnel as well as providing qualitative teaching and learning environment for students. This scenario undoubtedly is becoming a recurring decima as management of public universities become handicapped as it were due largely to political meddlesomeness with regards to financial autonomy, improper planning and inadequate funding that have become a clog in the wheel of progress of many public University management. Therefore, this study examines the impact of financial autonomy, improper planning and inadequate funding with emphasis on effective management of public Universities in Nigeria and came up with the suggestion that for effective management to be achieved and sustained, management of public universities in Nigeria must give adequate attention to financial autonomy, proper planning and funding.