The aerodynamic modelling is one of the challenging tasks that is generally established using the results of the computational fluid dynamic software and wind tunnel analysis performed either on the scaled model or the prototype. In order to improve the confidence of the estimates, the conventional parameter estimation methods such as equation error method (EEM) and output error method (OEM) are more often applied to extract the aircraft’s stability and control derivatives from its respective flight test data. The quality of the estimates gets influenced due to the presence of the measurement and process noises in the flight test data. With the advancement in the machine learning algorithms, the data driven methods have got more attention in the modelling of a system based on the input-output measurements and also, in the identification of the system/model parameters. The research article investigates the longitudinal stability and control derivatives of the aerodynamic models by using an integrated optimisation algorithm based on a recurrent neural network. The flight test data of Hansa-3 and HFB 320 aircraft were used as case studies to see the efficacy of the parameter estimation algorithm and further, the confidence of the estimates were demonstrated in terms of the standard deviations. Finally, the simulated variables obtained using the estimates demonstrate a qualitative estimation in the presence of the noise.