Due to the accident at the Fukushima Nuclear Power Plant (NPP) following the Great East Japan Earthquake on March 11, 2021, residents of the coastal areas of Fukushima Prefecture were forced to evacuate due to the effects of radiation and their lifestyles have changed dramatically. Therefore, we conducted the Comprehensive Health Check (CHC) of the Fukushima Health Management Survey (FHMS) to assess the health status of residents in the evacuation area and to prevent lifestyle-related diseases. First, to examine the short- to mid-term effects of the NPP accident, pre- and post-disaster data on health checkup of the evacuation area residents were retrospectively analyzed. Next, to examine the mid- to long-term effects of the NPP accident, we prospectively examined health examination data during the post-disaster period (fiscal year (FY) 2011–2017). The subjects were men and women living in 13 municipalities in the area surrounding the NPP in Fukushima Prefecture. We analyzed 27,486 men and women (12,432 men and 15,054 women) aged 20 years or older for whom health checkup data were available before and after the disaster, and found that the proportion of obese people and the prevalence of hypertension, dyslipidemia, diabetes mellitus, metabolic syndrome, liver dysfunction, hyperuricemia, polycythemia, and atrial fibrillation were increased after the disaster (FY2011–2012), compared with those before the disaster (FY 2008–2010). This trend was more pronounced among residents who were forced to evacuate. The analysis of 27,536 people (12,254 men and 15,282 women) who could be followed for an average of 5.5 years from FY 2011 to FY 2017 showed that the proportion of obese people remained unchanged, while the proportion of people with liver dysfunction decreased. The prevalence of hypertension, dyslipidemia, and diabetes increased further. Furthermore, evacuees were shown to be at higher risk of developing diabetes, dyslipidemia, chronic kidney disease, hypertension, and hepatic dysfunction than non-evacuees. On the other hand, regular exercise was a significant preventing factor for liver dysfunction and dyslipidemia. Since residents in the evacuation areas, especially evacuees, continue to be at high risk of developing lifestyle-related diseases, especially cardiovascular diseases, it is necessary to management their health status over a long period of time and implement preventive measures against lifestyle-related diseases.