Fishes in the genus Scomber are currently one of the most abundant, economically important, and widely distributed fishes in the North Pacific and North Atlantic Oceans. This study recorded the depth, peritoneal and environmental temperature of the chub mackerel Scomber japonicus using an electronic tag. The 176 tagged mackerel were released from Tsushima Strait, Japan. A total of 1,075 days of data from November to August were obtained from seven individuals. Mackerel extensively used the epipelagic zone, and ranges of depth and environmental temperature during the overall recording period were 0.5–213 m and 3.4–29.1 °C, respectively. The mean depth during the day was deeper than that observed during the night in the foraging season. This vertical distribution pattern of the mackerel may overlap with that of prey organisms. We also observed a unique short-term vertical migration of mackerel during the foraging season. When the mackerel repeated the short-term vertical migrations, ranges of peritoneal temperature (13.9–15.0 °C) were narrower than environmental temperature (7.9–16.5 °C). This behavior allowed the mackerel to use physiologically unsuitable thermal layers, while avoiding overcooling of body temperature. However, these vertical migration patterns broke down in the spawning season. Behavioral decisions of diel vertical migration in chub mackerel may be affected by body condition of individual fish such as maturation states. Quantifying vertical migrations of Scomber species occupying intermediate trophic levels is important when considering conservation strategies of more than simply fisheries stock but also that of marine ecosystems.