Alien mammal species have a very long history of anthropogenic introductions and have been extensively studied due to their severe impact on native biodiversity and ecosystems. One of the most detrimental species is the sika deer (Cervus nippon), a native Asian deer that has settled in several districts of the Czech Republic and has widely colonized the area with increasing population numbers. In this study we aimed to investigate the trend of the number of sika deer culled in the country between 1994 and 2018, and to highlight limits and flaws in the current management and hunting strategy. We identified three hunting subpopulations based on both the official hunting records and the environmental and urban features of the Czech Republic. The analyses of the subpopulations over the period between 1994 and 2018 revealed very different trends, some of which are alarming. The average annual increase in culling was 7.4% for Subpopulation 1 (SP1), 1% for Subpopulation 2 (SP2), and 3.7% for Subpopulation 3 (SP3). Considered the increased percentages of culled deer, and the environmental features of the country, we evaluated the central subpopulation (SP2) as the easiest to manage due to its small area of extension, the scarcity of forested regions and, as possible contribution, the natural occurrence of predators. Being the other two subpopulations spread across larger forested areas and hosting a higher number of deer, we concluded that an increasing effort, and a more well-designed strategy to ensure accuracy of hunting plans seems to be impelling for the country.