A time-varying model for the forward flight dynamics of a flapping-wing micro aerial vehicle is determined from free-flight optical tracking data using system identification. Based on timescale separation, the aerodynamic forces and moments are each formulated as a linear addition of decoupled time-averaged and time-varying sub-models. The aerodynamic models are incorporated in linearised equations of motion, resulting in an accurate and simulation-capable dynamic model. The time-averaged component is assumed to be linear; the time-varying component is represented as a third-order Fourier series, which effectively approximates the flapping dynamics. Combining both components yields a more complete and realistic simulation. The model is used to assess the validity of the widely-applied timescale separation assumption and results suggest that while in steady flight the assumption applies well, during manoeuvres the time-varying dynamics are not fully captured. More accurate modelling of flapping-wing flight during manoeuvres may require more advanced models that consider coupling between the time scales. Nomenclature f = frequency, Hz F = aerodynamic forces, N , and moments, N m g = acceleration due to gravity, ms −2 I x , I z , I xz = body moments of inertia, kg · m 2 J = cost function L, M, N = aerodynamic moments around x b , y b and z b axis, N m m = mass, kg n k = number of measurement points n u , n x , n y = number of inputs u, states x, outputs y p, q, r = turn rates in body-fixed coordinates, rad · s −1 R = measurement error covariance matrix u, v, w = velocities in body-fixed coordinates ms −1 u = model input x b , y b , z b = body-fixed coordinate system x = state vector y = model-predicted system output z = measured system output X, Y, Z = aerodynamic forces along x b , y b and z b axis, N α, β = angle of attack, angle of sideslip, rad δ e , δ r = elevator deflection, rudder deflection, radˆΘ = parameter estimates Φ, Θ, Ψ = Euler angles, rad