A superconductor, when exposed to a spin-exchange field, can exhibit spatial modulation of its order parameter, commonly referred to as the Fulde–Ferrell–Larkin–Ovchinnikov state. Such a state can be induced by controlling the spin-splitting field in Josephson junction devices, allowing access to a wide range of the phase diagram. Here we demonstrate that a Fulde–Ferrell–Larkin–Ovchinnikov state can be induced in Josephson junctions based on the two-dimensional dilute magnetic topological insulator (Hg,Mn)Te. We do this by observing the dependence of the critical current on the magnetic field and temperature. The substitution of Mn dopants induces an enhanced Zeeman effect, which can be controlled with high precision by using a small external magnetic field. We observe multiple re-entrant behaviours of the critical current as a response to an in-plane magnetic field, which we assign to transitions between ground states with a phase shifted by π. This will enable the study of the Fulde–Ferrell–Larkin–Ovchinnikov state in much more accessible experimental conditions.