This paper explains how to construct the municipality-level panel data in Japan in the period of 1980–2020. Municipal mergers conducted around 2005, which is known as “Great Mergers in the Heisei era,” result in reduction of almost half of the number of Japanese municipalities. The big change in shapes of municipalities by these municipal merges causes difficulties in constructing municipality-level panel data. To address this problem, this paper proposes a method of aggregating municipal districts in the past by identical geographical unit throughout the period. The converter file made in this paper is distributed to the public.