Conflict resolution problem can be solved using three different approaches: airspeed change (SC), heading angle change (HAC), and flight level change (FLC). SC and HAC do not affect the vertical position of aircraft; however, changing the flight level of an aircraft causes an interaction between different levels. Also, the wind effect may change between the levels, which can affect the aircraft’s ground speeds. In such a situation, controllers may need to intervene to ensure minimum separations between aircraft. Even though FLC is performed with a single instruction, conflict resolution using this approach creates follow-up difficulties for the controllers. This study develops a stochastic conflict resolution algorithm by considering the FLC instructions to help the controller decisions. To find out the possible benefits of the model, it is compared to deterministic and expected value approaches. Real wind data is obtained from the weather sound database and integrated into the model. Both wind speed and wind direction uncertainties are considered, and the differences between the wind speeds for different levels are reflected in the model as coefficients. As a result, the presented model provided an average of 4.17% fuel savings compared to the deterministic approach and resulted with resilient solutions applicable under wind uncertainties.