Since the Great East Japan Earthquake in March 2011, an increase in lifestyle-related diseases due to changes in living environment following the nuclear power plant accident has been reported in Fukushima Prefecture, especially among evacuees. However, no long-term studies covering the entire Fukushima Prefecture have been conducted. The study aim was to investigate the effects of post-disaster evacuation life on the prevalence of dyslipidemia in Fukushima Prefecture using a national database. The data from 3,866,674 people who underwent specific health checkups between fiscal year (FY) 2008 and FY2017 were analyzed. Fukushima Prefecture was divided into four areas, and the prevalence of dyslipidemia and related parameters were compared. The prevalence of dyslipidemia increased overall, with a particularly sharp increase after FY2011 in the evacuation area. The sex- and age-adjusted odds ratio (95% confidence intervals) of having dyslipidemia in the evacuation area compared with that in the control area was 0.951 (0.929–0.973) in FY2008–2010, which increased to 1.130 (1.105–1.155) in FY2012–2014 and 1.117 (1.092–1.143) in FY2015–2017. Since the prevalence of dyslipidemia has increased and remained high after the earthquake in Fukushima Prefecture, especially in the evacuation area, continued measures to prevent cardiovascular diseases among the residents are needed.