To screen various pomegranate rootstocks for drought tolerance, this research was undertaken to investigate the phytochemical changes in the leaves of nine pomegranate rootstocks (‘Daneshgah 5’, ‘Daneshgah 8’, ‘Daneshgah 13’, ‘Daneshgah 19’, ‘Daneshgah 22’, ‘Daneshgah 25’, ‘Daneshgah 28’, ‘Daneshgah 32’ and ‘Daneshgah 40’) under well-watered and drought-stressed conditions. The rootstocks were exposed to drought stress by stopping irrigation for 20 days. Under drought stress conditions, various pomegranate rootstocks showed apparent differences in phytochemical compounds. Among the evaluated rootstocks, ‘Daneshgah 13’ and ‘Daneshgah 32’exhibited good tolerance to drought stress due to the smaller reductions in leaf relative water content (LRWC), more values of chlorophyll, soluble proteins, proline, total phenol, the activity of guaiacol peroxidase (GPX) and catalase (CAT) enzymes, as well as lower values of malondialdehyde (MDA) and hydrogen peroxide (H2O2). Therefore, ‘Daneshgah 13’ and ‘Daneshgah’ can be used in promoting the yield of pomegranate in drought-prone regions and as appropriate genetic resources in breeding programs for tolerance to drought.