Cooperative Intelligent Transport System (C-ITS) plays a vital role in the future road traffic management system. A vital element of C-ITS comprises vehicles, road side units, and traffic command centers, which produce a massive quantity of data comprising both mobility and service-related data. For the extraction of meaningful and related details out of the generated data, data science acts as an essential part of the upcoming C-ITS applications. At the same time, prediction of short-term traffic flow is highly essential to manage the traffic accurately. Due to the rapid increase in the amount of traffic data, deep learning (DL) models are widely employed, which uses a non-parametric approach for dealing with traffic flow forecasting. This paper focuses on the design of intelligent deep learning based short-term traffic flow prediction (IDL-STFLP) model for C-ITS that assists the people in various ways, namely optimization of signal timing by traffic signal controllers, travelers being able to adapt and alter their routes, and so on. The presented IDL-STFLP model operates on two main stages namely vehicle counting and traffic flow prediction. The IDL-STFLP model employs the Fully Convolutional Redundant Counting (FCRC) based vehicle count process. In addition, deep belief network (DBN) model is applied for the prediction of short-term traffic flow. To further improve the performance of the DBN in traffic flow prediction, it will be optimized by Quantum-behaved bat algorithm (QBA) which optimizes the tunable parameters of DBN. Experimental results based on benchmark dataset show that the presented method can count vehicles and predict traffic flow in real-time with a maximum performance under dissimilar environmental situations. 20