This study used the data from the 2015 OECD Programme for International Student Assessment (PISA) to examine the relationship between perceived teacher unfairness and science achievement with a three-level hierarchical linear model (HLM) as the analytic approach. Data of 188,104 students from 4895 schools in 52 countries and economies were used for analysis. After accounting for student gender, student-, school-, and country-level economic, social, and cultural status, and students' non-cognitive outcomes, the results of HLM analysis showed that perceived teacher unfairness negatively predicted science achievement with a modest effect size. The possible explanations of the results and the practical implication of the findings were discussed.