A programmable Josephson voltage standard (PJVS) can be used to generate a precision square wave for induced voltage compensation to measure the mutual inductance between the coils in a joule balance. In this paper, the influence of the transitions between quantized voltages in the synthesized square waves is analyzed in detail. The ratio of the time-integrated value of the transitions to the total waveform is reduced to several parts in 104 to improve the measurement accuracy. The influence of different configurations of the integrating digitizer is discussed. The result shows that when the voltages are in a quantum state, the time-integrated agreement between the measured and theoretical differences for two PJVS systems is within 4 × 10−9 V s V−1 s−1. For the total time integration of a voltage waveform larger than 2 V s, the combined relative uncertainty is less than 5.9 × 10−8 V s V−1 s−1. The result confirms the capability of the PJVS to generate a precision square wave for the joule balance.