Introduction: The study examined the relationship between budgeting/budgetary control system and institutional effectiveness in Universities in Kwara State, Nigeria. Purpose: The purpose of the study was to examine the impact of budget committee, budget implementation, value for money check and internal audit check on institutional effectiveness in universities in Kwara State. Methodology: Two researchers’ questionnaires were designed to collect data from sampled respondents; they were ‘Budgeting/Budgetary control System Questionnaire (BBCSQ)’ and ‘Institutional Effectiveness Questionnaire (IEQ)’. The instruments were validated by two experts to ascertain the content validity while the reliability of the instruments was determined using Cronbach Alpha statistics, thus, the reliability coefficients were found to be 0.83 and 0.76 respectively. Four universities were randomly sampled out of the six accredited universities in Kwara State. The selection represented 67% of the total population. The respondents were the staff of the bursary department of the sampled universities and 110 respondents were determined out of the 290 targeted population using proportional sampling technique. The data collected were analyzed using SPSS version 21.0 at 0.05 level of significant using PPMC while descriptive statistics of means and standard deviation were used to answer the research questions raised in the study. Results: The result of the study revealed that there was a significant relationship between budgeting/budgetary control system and institutional effectiveness in Universities in Kwara State (r. value=.578> t. value=.000). Recommendations: It was recommended among others that budget committee should be composed of experienced and well versatile members in the field of accounting and finance to enhance their performance and overall effectiveness in the system.