Unmanned Aerial Vehicles (UAVs) are important tool for various applications, including enhancing target detection accuracy in various surface-to-air and air-to-air missions. To ensure mission success of these UAVs, a robust control system is needed, which further requires well-characterized dynamic system model. This paper aims to present a consolidated framework for the estimation of an experimental UAV utilizing flight data. An elaborate estimation mechanism is proposed utilizing various model structures, such as Autoregressive Exogenous (ARX), Autoregressive Moving Average exogenous (ARMAX), Box Jenkin’s (BJ), Output Error (OE), and state-space and non-linear Autoregressive Exogenous. A perspective analysis and comparison are made to identify the salient aspects of each model structure. Model configuration with best characteristics is then identified based upon model quality parameters such as residual analysis, final prediction error, and fit percentages. Extensive validation to evaluate the performance of the developed model is then performed utilizing the flight dynamics data collected. Results indicate the model’s viability as the model can accurately predict the system performance at a wide range of operating conditions. Through this, to the best of our knowledge, we present for the first time a model prediction analysis, which utilizes comprehensive flight dynamics data instead of simulation work.