The relationship between the Madden–Julian oscillation (MJO) and the seasonal cycle of the intraseasonal rainfall variability in the Amazon Basin (AB) are analysed using band-pass-filtered gauge-based gridded rainfall data for the 1980–2009 period. Intraseasonal events (IE) have been defined and selected based on extreme values of the first principal component (PC1) time series, which comes from the empirical orthogonal function (EOF) analysis applied to the filtered rainfall data over the AB. A total of 132 IEs were identified with an average of approximately five events per year. About 25% of the total IEs in the Amazon region are not restricted to the eastwards propagating equatorially confined MJO and other mechanisms (e.g., through Rossby wave trains in the Southern Hemisphere) might play an important role. In addition, we find that the incomplete IEs (events that do not evolve through a complete life cycle) are associated with suppressed rainfall conditions over tropical South America. The development of the IEs over the AB, when compared with the different phases of the MJO index, shows a coherent relationship, where convective-based indices are able to better account their evolution. On a global scale, the upper-tropospheric patterns and the rainfall composites based on the PC1 time series show that the MJO is one of the main atmospheric modulator mechanisms of the intraseasonal rainfall variability over the Amazon region throughout the annual cycle. It is found that the intraseasonal variability is particularly important during the austral winter, when the percentage contribution with respect to the mean daily seasonal precipitation over some Amazon regions can reach 50%.