Abstract Resistively shunted Nb/Al-AlO _x /Nb Josephson junctions have been widely used in large-scale superconducting electronics such as the single-flux quantum circuit. The critical current primarily determines the working margin of the circuit. The distribution of vortices in the niobium film around superconducting devices is also commonly suspected to degrade the performance of devices. Unfortunately, most studies on Nb/Al-AlO _x /Nb Josephson junctions only present electric transport measurements. Using a magnetic force microscope, we observed the static distribution of the vortices around the junction after sweeping the current–voltage curves of the junction in-situ. The measurements showed that the distribution density of vortices affected the critical current of the junction. Furthermore, we observed an aggregation of vortices arising from the Joule heat generated by the shunt resistor. This caused an irreversible decrease in the junction’s critical current.