Flight controllers of the International Space Station (ISS) are engaged in shift work to provide 24-h coverage to support ISS systems. The purpose of this study was to investigate the prevalence and associated factors of shift work sleep disorder (SWSD) among Japanese ISS flight controllers. A questionnaire study was conducted using the Standard Shiftwork Index to evaluate sleep-related problems and possible associated variables. Among 52 respondents out of 73 flight controllers, 30 subjects were identified as night shift workers who worked 3 or more night shifts per month. Those night shift workers who answered “almost always” to questions about experiencing insomnia or excessive sleepiness in any case of work shifts and days off were classified as having SWSD. Additionally, 7 night shift workers participated in supplemental wrist actigraphy data collection for 7 to 8 days including 3 to 4 days of consecutive night shifts. Fourteen of 30 night shift workers were classified as having SWSD. Significant group differences were observed where the SWSD group felt that night shift work was harder and reported more frequent insomniac symptoms after a night shift. However, no other variables demonstrated remarkable differences between groups. Actigraphy results characterized 5 subjects reporting better perceived adaptation as having regular daytime sleep, for 6 to 9 h in total, between consecutive night shifts. On the other hand, 2 subjects reporting perceived maladaptation revealed different sleep patterns, with longer daytime sleep and large day-to-day variation in daytime sleep between consecutive night shifts, respectively. As the tasks for flight control require high levels of alertness and cognitive function, several characteristics, namely shift-working schedule (2 to 4 consecutive night shifts), very short break time (5 to 10 min/h) during work shifts, and cooperative work with onboard astronauts during the evening/night shift, accounted for increasing workloads especially in the case of night shifts, resulting in higher or equal prevalence of SWSD to that among other shift-working populations. Further studies are required to collect more actigraphy data and examine the possibility of interventions to improve SWSD.