The objective of this study is to determine the height of the atmospheric boundary layer and to identify its temporal and spatial variations over Iran. Monthly atmospheric boundary layer height (ABLH) data from the European Centre for Medium-Range Weather Forecasts (ECMWF) ERA-Interim dataset with spatial resolution of 0.125° was used during the period from 1/1979 to 12/2016. Hierarchical clustering analysis was utilized to identify the homogeneous regions of the boundary layer height. Five distinct and homogenous regions were recognized. The nonparametric modified Mann-Kendall and the Sen’s slope estimator tests were applied to detect significant trends and changes rate, respectively. The results showed that ABLH has increased significantly over Iran during the study period at 95% confidence level with increase of about 3.1 m per year. Large ABLH increases (140–160 m.decade−1) occurred over the semi-northern part of country especially in leeward regions of Alborz Mountains range. We also found abrupt upward changes in the ABLH in 1998. Annual variations of ABLH show a strong positive correlation with air temperature and strong negative correlation with surface relative humidity.