A theoretical and experimental analysis of the impact of pulse modulation format on Brillouin optical time-domain analysis (BOTDA) sensors using pulse coding techniques has been carried out. Pulse coding with conventional non-return-to-zero (NRZ) modulation format is shown to induce significant distortions in the measured Brillouin gain spectrum (BGS), especially in proximity of abrupt changes in the fiber gain spectra. Such an effect, as confirmed by the theoretical analysis, is due to acoustic wave pre-excitation and non-uniform gain which depends on the bit patterns defined by the different codewords. A successful use of pulse coding techniques then requires to suitably optimize the employed modulation format in order to avoid spurious oscillations causing severe penalties in the attained accuracy. Coding technique with return-to-zero (RZ) modulation format is analyzed under different duty-cycle conditions for a 25 km-long sensing scheme, showing that low duty-cycle values are able to effectively suppress the induced distortions in the BGS and allow for spatially-accurate, high-resolution strain and temperature measurements being able to fully exploit the provided coding gain (~7.2 dB along 25 km distance) with unaltered spatial resolution (1 meter). Although Simplex coding is used in our analysis, the validity of the results is general and can be directly applied to any intensity-modulation coding scheme.