We apply the method of flow equations to describe quantum systems subject to a time-periodic drive with a time-dependent envelope. The driven Hamiltonian is expressed in terms of its constituent Fourier harmonics with amplitudes that may vary as a function of time. The time evolution of the system is described in terms of the phase-independent effective Hamiltonian and the complementary micromotion operator that are generated by deriving and solving the flow equations. These equations implement the evolution with respect to an auxiliary flow variable and facilitate a gradual transformation of the quasienergy matrix (the Kamiltonian) into a block-diagonal form in the extended space. We construct a flow generator that prevents the appearance of additional Fourier harmonics during the flow, thus enabling implementation of the flow in a computer algebra system. Automated generation of otherwise cumbersome high-frequency expansions (for both the effective Hamiltonian and the micromotion) to an arbitrary order thus becomes straightforward for driven Hamiltonians expressible in terms of a finite algebra of Hermitian operators. We give several specific examples and discuss the possibility to extend the treatment to cover rapid modulation of the envelope.