Past studies presented evidence that deforestation may affect the precipitation seasonality in southern Amazon. This study uses daily rainfall data from Tropical Rainfall Measurement Mission 3B42 product and a recent yearly 1‐km land use dataset to evaluate the quantitative effects of deforestation on the onset, demise and length of the rainy season in southern Amazon for a period of 15 years (1998–2012). Additionally, we use the Niño4 index, zonal wind data and deforestation data to explain and predict the interannual variability of the onset of the rainy season. During this period, onset has delayed ~0.38 ± 0.05 days per year (5.7 ± 0.75 days in 15 years), demise has advanced 1.34 ± 0.76 days per year (20 ± 11.4 days in 15 years) and the rainy season has shortened by 1.81 ± 0.97 days per year (27 ± 14.5 days in 15 years). Onset, demise and length also present meridional and zonal gradients linked to large‐scale climate mechanisms. After removing the effects related to geographical position and year, we verified a relationship between onset, demise and length and deforestation: Onset delays ~0.4 ± 0.12 day, demise advances ~1.0 ± 0.22 day and length decreases ~0.9 ± 0.34 day per each 10% deforestation increase relative to existing forested area. We also present empirical evidence of the interaction between large‐scale and local‐scale processes, with interannual variation of the onset in the region explained by Niño4 sea surface temperature anomalies, Southern Hemisphere subtropical jet position, deforestation and their interactions (r2 = 69%, p < .001, mean absolute error = 2.7 days).