Short-rotation plantations are extending worldwide due to the increased demand for pulp and wood. Reliable estimations of recent expansion of short-rotation plantation areas and associated land use changes are a prerequisite to assess their environmental impact on regional carbon and water cycles, and on climate. A binary classification methodology using MODerate resolution Imaging Spectroradiometer (MODIS) 16-day 250 m NDVI time series was developed and applied to classify Eucalyptus plantations across Brazil. The identification of Eucalyptus plantations specific patterns in the time series was based on the calculation of matching functions between the NDVI time series and a ~ 2 years long reference time series. Among the seven tested matching functions, the bounding envelope was the most successful. This method was robust to residual noise on the NDVI time series, and a threshold coefficient for the binary classification was adjusted using an omission-commission criteria. With this method, it was possible to detect any presence of Eucalyptus between 2003 and 2009 at monthly time-steps, including the periods of bare soils between two rotations that are typically 6-7 years long. The dates of first afforestation, of clear-cut at the end of a rotation, and of re-planting at the beginning of a new rotation were retrieved from the NDVI time series with a precision of ~ 66 days. The final almost continuous tri-dimensional map (space and time) was validated with three different datasets, from local to regional data. All three datasets gave similarly high global accuracy statistics, but a global underestimation of Eucalyptus areas compared to large scales census was observed. Discrepancies and way to improve the Eucalyptus area estimates were discussed in this study. The developed methodology could be applied to other short-rotation tree plantations.