The study analyzes student, school and district level inequalities of Albanian education system as evidenced in two large-scale assessments. Two main datasets were used for this study, PISA 2018 and the Albanian State Matura Exam 2017. Due to the limited availability of data, the study could only consider a small number of dependent variables at the individual, school, and district level. Utilizing a multilevel analysis, the study observes considerable differences among schools and districts in all three PISA domains and the State Matura Exam. The results were inconclusive regarding shortages of resources at the school and district level. Staff shortage was associated with academic performance in the PISA 2018 dataset, but no statistical association could be identified with the lack of school resources. The analysis of the district financial resources did not show any significant relationship between spending and school performance in the Albanian State Matura Exam. Gender disparities were present in both datasets. Socioeconomic factors, which were measured only in the PISA dataset, had an effect on the student’ achievement.