In Taiwan, immigrant workers play an important role in fisheries but they are easily ignored by society. The health problems and associated characteristics of immigrant workers in fisheries remain unclear. Descriptive and retrospective analyses were performed. Outpatient data were collected from a primary care clinic for six fishing villages in North Eastern Taiwan between 1 August 2016 and 31 July 2017. The data of immigrant workers was recorded and compared with that of natives. A total of 241 immigrant workers and 1342 natives were enrolled. Compared with the natives, the immigrant workers had a significantly younger age, male predominance, and fewer mean visits per year. The immigrant worker’s visits tended to be more highly focused during the third quarter of the year. Immigrant workers paid more registration fees and self-payment, but they paid less on diagnosis fees, oral medication, laboratory exams and had reduced total costs. The top five diagnoses for immigrant workers were respiratory diseases (38.3%), trauma (15.2%), musculoskeletal diseases (11.2%), skin-related diseases (9.5%), and digestive diseases (9.1%). Immigrant workers were positively correlated with infectious/parasitic diseases, and negatively correlated with medical consults and endocrine/metabolic diseases. Immigrant workers were also positively associated with registration fees and self-payment, but negatively correlated with diagnosis fees and total costs (all p < 0.05). The distribution of skin diseases and trauma were affected by age and sex as opposed to ethnic group. Immigrant status’ health issues should be given more attention.