Matsunaga was educated at and played for Hamana High School and Aichi Gakuin University. After graduating from the university, he joined Japan Soccer League club Nissan Motors (later "Yokohama Marinos") in 1985. The club also won 1985 Emperor's Cup. From 1988 to 1990, the club won all three major title in Japan; Japan Soccer League, JSL Cup and Emperor's Cup for 2 years in a row. In 1990s, the club won 1990 JSL Cup, 1991 and 1992 Emperor's Cup. In Asia, the club won 1991–92 Asian Cup Winners' Cup.