Abstract The temporal evolution of antiferromagnetic domain pattern changes under resonant excitation of the second-order transverse optical (2TO) phonon mode in nickel oxide was investigated using mid-infrared free electron laser (MIR-FEL) pulses and visible nanosecond probe laser pulses at room temperature. We visualized the domain patterns through magneto-optical polarized microscopy in transmission and observed their temporal variation after the phonon excitation via MIR-FEL. We evaluated the differences throughout the timeline using the structural similarity index measure (SSIM) technique from domain images with and without MIR-FEL irradiation. We found that the MIR-FEL irradiation induces significant structural changes in the domain patterns. The maximum difference was observed at the timing of the MIR-FEL irradiation and exponentially recovered with the time constant of 1.4 ± 0.2 ms. This rather long-time constant could be owing to the spin relaxation, whilst further investigation is needed to confirm the underlying mechanism.