The passenger prediction flow is very significant to transportation sustainability. This is due to some chaos of traffic jams encountered by the road users during their movement to the offices, schools, or markets at earlier of the days and during closing periods. This problem is peculiar to the transportation system of the Federal University of Technology Minna, Nigeria. However, the prevailing technique of passenger flow estimation is non-parametric which depends on the fixed planning and is easily affected by noise. In this research, we proposed the development of a hybrid intelligent passenger frequency prediction model using the Auto-Regressive Integrated Moving Average (ARIMA) linear model, Convolutional Neural Network (CNN), and Kalman Filter Algorithm (KFA). The passengers’ frequency of arrival at the bus terminals is obtained and enumerated through the closed-circuit television (CCTV) and demonstrated using the Markovian Queueing Systems Model (MQSM). The ARIMA model was used for learning and prediction and compared the result with the combined techniques of using CNN-KFA. The autocorrelation coefficient functions (ACF) and partial autocorrelation coefficient functions (PACF) are used to examine the stationary data with different features. The performance of the models was analyzed and evaluated in describing the short-term passenger flow frequency at each terminal using the Mean Absolute Percentage Error (MAPE) and Mean Squared Error (MSE) values. The CNN-Kalman-filter model was fitted into the short-term series and the MAPE values are below 10%. The Mean Square Error (MSE) shows that the CNN-Kalman Filter model has the overall best performance with 83.33% of the time better than the ARIMA model and provides high accuracy in forecasting.