Objective To analyze the epidemic status of imported malaria at different stages of malaria elimination program in Fujian Province, in order to provide scientific basis for the formulation of malaria prevention and control strategy and implementation of control measures in later stage of elimination efforts. Methods The process of malaria elimination in Fujian Province was divided into three stages: the pre-elimination stage from 2005 to 2009, the elimination stage from 2010 to 2015, and the post-elimination stage from 2016 to 2019. Data of malaria cases and epidemiological investigations at different stages were collected to analyze the epidemic situation of imported malaria cases using SPSS 17.0 software. Results A total of 1 105 malaria cases were reported in Fujian Province from 2005 to 2019, and all were imported cases except for 3 locally transmitted cases. The annual average number of imported cases reported in the post-elimination stage (116.3 cases per year) was higher than those in the elimination (74.2 cases) and the pre-elimination (38.4 cases) stages. The proportion of falciparum malaria cases increased with staging, from 21.9% (42/192) in the pre-elimination stage, to 60.9% (271/445) in the elimination stage, and to 76.8% (357/465) in the post-elimination stage (P < 0.01). With regard to the infection source, there were cases with a source of local transmission in the pre-elimination and elimination stages, while in the post-elimination stage all cases were imported from abroad, among the imported, the case proportion from Africa increased from 27.1% (52/192) in the pre-elimination stage to 75.7% (337/445) in the elimination stage and to 92.3% (429/465) in the post-elimination stage (P < 0.01). The proportion of cases reported from medical institutions increased, which was significantly higher in the post-elimination stage (95.1%, 442/465) than in the elimination (65.6%, 292/445) and pre-elimination stages (65.1%, 125/192) (P < 0.01). There was an obvious seasonal distribution of reported cases in the pre-elimination stage (peak occurred in summer), but not in the elimination stage, while in the post-elimination stage the reporting peak occurred in the beginning of the year (January-February) and the middle of the year (June-July). The regional distribution of reported cases in three stages found that the reporting was mainly concentrated in Fuzhou, but the proportion increased, showing the proportion in the pre-elimination, elimination and post-elimination stages was 35.9% (69/192), 72.8% (324/445) and 78.1% (363/465) respectively, with statistically significant differences (P < 0.01). The age distribution revealed that the cases were largely in young and middle-aged males (20-59 years old), accounting the proportions in the elimination and post-elimination stages were 96.2% (428/445) and 96.1% (447/465), both higher than 83.3% (160/192) in the pre-elimination stage(P < 0.01). Conclusion During the malaria post-elimination stage, there is a more severe challenge of imported malaria in Fujian Province, especially falciparum malaria imported from Africa, thus public health education to key population and training for medical institutions should be strengthened.