The leishmaniases are severe parasitic diseases that occur worldwide, caused by protozoa of the genus Leishmania. Studies with medicinal plants can lead to a range of possibilities for treating and improving the patients' quality of life. Research on Azadirachta indica fractions and extracts has shown that they have excellent anti-leishmanial activity based on bioactivity-guided fractionation of ethanolic extracts of leaves and seeds and in vitro activity against promastigotes. In this research the most efficient extracts and fractions were selected for tests on intracellular amastigotes of Leishmania amazonensis. The ethanolic extract of the leaves and dichloromethane and chloroform fractions had IC50 values of 38, 3.9 and 1.2 μg/mL for promastigotes and 9.8, 1.1 and 0.6 μg/mL for amastigotes, respectively, at 72 hours. For the ethanolic extract and dichloromethane fraction from nut tegument, the IC50 was 2.7 and 2.1 μg/mL for promastigotes and 0.4 and 0.6 μg/mL for amastigotes. The cytotoxicity of the fractions presented selectivity that was between 8 to 32 times more toxic to promastigotes and 15 to 72 times to amastigotes than to macrophages. The extracts and fractions from leaves and fruits were more effective against amastigotes, and the fractionation increased activity against both promastigotes and amastigotes, enabling us to obtain potentially active fractions with low toxicity.