Currently, quite accurate measurements of atmospheric gusts are carried out by airport systems only in the vicinity of the runways. There is a still open issue of availability of information about real wind gusts at cruising altitudes and during approach at a considerable distance from the airfield. Standard on-board systems of a jet transport airplane provide some information which is desirable to have knowledge of how flight parameters reflect real gust parameters and their impact on the aircraft dynamics. The paper proposes an algorithm for headwind gust magnitude estimation in relation to aircraft response. The analysed estimation algorithms assume the use of data available from the existing on-board systems only without the employment of any extra sensors or ground and satellite systems. In this way, many problems caused by different structures, configurations, and ways of installation of additional sensors and structural changes are rejected. The algorithms use the classical method for estimation of wind parameters as well as a linear longitudinal model of aircraft dynamics, taking into account the influence of wind gusts. Data fusion was realised with the use of three filtration methods. Results were evaluated to select the most accurate method of the estimation. Test data were obtained from advanced flight simulation. The experimental scenario considered a flight of a passenger twin-engine jet airplane through a layer of programmed gusts. The results of the flight simulations allowed us to determine the accuracy of the proposed gust estimation algorithms in reference to the ideal wind-speed data analysis obtained directly from the simulation environment (with the accuracy of the simulation process). The use of the proposed gust estimation algorithms may provide more accurate signal for integrated on-board systems, especially for wind shear detection and sped-up response time of flight control systems, protecting aircrafts against the adverse impact of encountered wind shear or gusts, e.g., auto-thrust or auto-throttle systems. The dedicated algorithm presented in the paper may increase the safety level of take-off and approach phases in gusty conditions and also during significant changes in wind speed at cruising altitudes in the case of crossing the area of jet stream occurrence.