The illustrations are of a wild bull and a Barbary sheep on the upper-arm of a male mummy, and S-shaped motifs on the upper-arm and shoulder of a female.
The discovery pushes back evidence for the practice in Africa by 1,000 years.
Details of the tattoos have been published in the Journal of Archaeological Science.
Previous CT scans showed that he was between 18 and 21 years old when he died from a stab wound to the back.
Dark smudges on his arm were thought to be unimportant until infrared scans revealed that they were tattoos of two slightly overlapping horned animals. One is interpreted to be a wild bull with a long tail and elaborate horns; the other appears to be a Barbary sheep with curving horns and a humped shoulder.
The designs are under the skin and the pigment is probably soot.
Previously, archaeologists had thought only women wore tattoos in the ancient past, but the discovery of tattoos on the male mummy now shows body modification concerned both sexes.
The mummies were found in Gebelein in the southern part of Upper Egypt, around 40km south of modern-day Luxor.
The individuals were buried in shallow graves without any special preparation, but their bodies were naturally preserved by the heat, salinity and aridity of the desert.
Radiocarbon results indicate that they lived between 3351 and 3017 BC, shortly before the region was unified by the first pharaoh at around 3100 BC.
The oldest example of tattooing is found on the Alpine mummy known as Ötzi who is thought to have lived between 3370 and 3100 BC. But his tattoos are vertical or horizontal lines, rather than figurative.