Inbreeding increases genome homozygosity within populations, which can exacerbate inbreeding depression by exposing homozygous deleterious alleles that are responsible for declines in fitness traits. In small populations, genetic purging that occurs under pressure of natural selection acts as an opposing force, contributing to a reduction of deleterious alleles. Both inbreeding and genetic purging are paramount in the field of conservation genomics. The Amur tiger (Panthera tigris altaica) lives in small populations in the forests of Northeast Asia and is among the most endangered animals on the planet. Using genome-wide assessment and comparison, we reveal substantially higher and more extensive inbreeding in wild Amur tigers (FROH = 0.50) than in captive individuals (FROH = 0.24). However, a relatively reduced number of loss-of-function mutations in wild Amur tigers is observed when compared with captive individuals, indicating a genetic purging of relatively large-effect inbreeding load. The higher ratio of homozygous mutation load and number of fixed damaging alleles in the wild population indicate a less-efficient genetic purging, with purifying selection also contributing to this process. These findings provide valuable insights for future conservation of Amur tigers.