El Niño is generally associated with negative rainfall anomalies (below-average rainfall) in northern Northeast Brazil (NNEB). In 2019, however, the opposite rainfall pattern was observed during an El Niño episode. Here, we explore the mechanisms that overwhelmed typical El Niño-related conditions and resulted in positive rainfall anomalies (above-average rainfall) in NNEB. We focus on the austral autumn when El Niño is most prone to rainfall anomalies in the region. The analysis of several datasets, including weather station data, satellite data, reanalysis data, and modelled data derived from a dry linear baroclinic model, allowed us to identify that the austral autumn 2019 above-average rainfall in NNEB was likely associated with four combined factors; these are (1) the weak intensity of the 2019 El Niño; (2) the negative phase of the Atlantic Meridional Mode; (3) local and remote diabatic heating anomalies, especially over the western South Pacific and tropical South Atlantic, which resulted in anticyclonic and cyclonic circulations in the upper and lower troposphere, respectively, over the tropical South Atlantic; and (4) sub-seasonal atmospheric convection anomalies over the western South Pacific, which reinforced the low-frequency convection signal over that region. This latter factor suggests the influence of the Madden–Julian Oscillation on rainfall in NNEB during the first ten days of March 2019. We discuss these mechanisms in detail and provide evidence that, even during an El Niño event, above-average rainfall in NNEB in the austral autumn may occur, and its modulation is not limited to the influence of a single climate phenomenon. Our results may assist in the planning of several crucial activities, such as water resources management and agriculture.