The synthesis of N–N axial compounds containing aromatic acyl amides using common acylation reagents remains challenging. We describe a highly atropenantioselective synthesis of N-aminoindoles containing N–N axes. A chiral cyclic isothiourea is used as the sole organic catalyst in the atropenantioselective transformation of the N-acylation reaction. Aroyl chlorides have been used as acylation reagents to construct atropisomeric compounds through N-acylation. The N-aminoindole products, which bear stereogenic N–N axes, were synthesized with high yields and enantioselectivities. Some of the enantiopure N-aminoindole products exhibited promising antibacterial activities against plant pathogens.