The atmospheric boundary layer height (zi) is a key parameter in the vertical transport of mass, energy, moisture, and chemical species between the surface and the free atmosphere. There is a lack of long-term and continuous observations of zi, however, particularly for remote regions, such as the Amazon forest. Reanalysis products, such as ERA5, can fill this gap by providing temporally and spatially resolved information on zi. In this work, we evaluate the ERA5 estimates of zi (zi-ERA5) for two locations in the Amazon and corrected them by means of ceilometer, radiosondes, and SODAR measurements (zi-experimental). The experimental data were obtained at the remote Amazon Tall Tower Observatory (ATTO) with its pristine tropical forest cover and the T3 site downwind of the city of Manaus with a mixture of forest (63%), pasture (17%), and rivers (20%). We focus on the rather typical year 2014 and the El Niño year 2015. The comparison of the experimental vs. ERA5 zi data yielded the following results: (i) zi-ERA5 underestimates zi-experimental daytime at the T3 site for both years 2014 (30%, underestimate) and 2015 (15%, underestimate); (ii) zi-ERA5 overestimates zi-experimental daytime at ATTO site (12%, overestimate); (iii) during nighttime, no significant correlation between the zi-experimental and zi-ERA5 was observed. Based on these findings, we propose a correction for the daytime zi-ERA5, for both sites and for both years, which yields a better agreement between experimental and ERA5 data. These results and corrections are relevant for studies at ATTO and the T3 site and can likely also be applied at further locations in the Amazon.