Dual flow auxiliary power unit (APU) inlets and associated systems and methods are disclosed. An inlet in accordance with one embodiment of the invention includes an entrance aperture and a divider positioned in the inlet and located to separate a first portion of the inlet from a second portion of the inlet. The first portion can be configured to couple to an engine air intake of an APU, and the second portion can be configured to direct air away from the air intake. The divider can be positioned to direct air having a first total pressure level and a first distortion level to the first portion of the inlet, and direct air having a second total pressure level and second distortion level to the second portion of the inlet. The first total pressure level can be approximately the same as or higher than the second total pressure level, or the second distortion level can be approximately the same as or higher than the first distortion level, or both.