Airlines tend to design their flights schedules with the primary concern of the minimization of operational costs. However, the recently emerging idea of resilient scheduling defined as staying operational in case of unexpected disruptions and adaptability should be of great importance for airlines as well due to the high opportunity costs caused by the flight cancellations and passenger inconvenience caused by delays in the schedule. In this study, we integrate resilient airline schedule design, aircraft routing and fleet assignment problems with uncertain non-cruise times and controllable cruise times. We follow a data-driven method to estimate flight delay probabilities to calculate the airport congestion coefficients required for the probability distributions of non-cruise time random variables. We formulate the problem as a bi-criteria nonlinear mixed integer mathematical model with chance constraints. The nonlinearity caused by the fuel consumption and CO2 emission function associated with the controllable cruise times in our first objective is handled by second order conic inequalities. We minimize the total absolute deviation of the aircraft path variability’s from the average in our second objective to generate balanced schedules in terms of resilience. We compare the recovery performances of our proposed schedules to the minimum cost schedules by a scenario-based posterior analysis.