Magnetic skyrmions are topological solitons with a nanoscale winding spin texture that hold promise for spintronics applications1-4. Skyrmions have so far been observed in a variety of magnets that exhibit nearly parallel alignment for neighbouring spins, but theoretically skyrmions with anti-parallel neighbouring spins are also possible. Such antiferromagnetic skyrmions may allow more flexible control than conventional ferromagnetic skyrmions5-10. Here, by combining neutron scattering measurements and Monte Carlo simulations, we show that a fractional antiferromagnetic skyrmion lattice is stabilized in MnSc2S4 through anisotropic couplings. The observed lattice is composed of three antiferromagnetically coupled sublattices, and each sublattice is a triangular skyrmion lattice that is fractionalized into two parts with an incipient meron (half-skyrmion) character11,12. Our work demonstrates that the theoretically proposed antiferromagnetic skyrmions can be stabilized in real materials and represents an important step towards their implementation in spintronic devices.