The friction coefficient in many friction stir welding researches is generally used as an effective, constant value without concern on the adaptable and changeable nature of the friction during welding sequence. This is understandable because the main problem in analyzing friction in friction stir welding are complex nature of the friction processes, case-dependent and time dependent contact between the bodies, influence of the temperature, sliding velocity, etc. This paper is presenting a complex experimental-numerical-analytical model for estimating the effective friction coefficient on contact of the bobbin tool and welding plates during welding, considering the temperature at the contact as the most influencing parameter on friction. The estimation criterion is the correspondence of the experimental temperature and temperature from the numerical model. The estimation procedure is iterative and parametric - the heat transport parameters and friction coefficient are adapted during the estimation procedure in a realistic manner to achieve relative difference between experimental and model's temperature lower than 3%. The results show that friction coefficient varies from 0.01 to 0.21 for steel-aluminium alloy contact and temperature range from 406 °C to 22 °C.