► We screened 20 induced mutants of sesame (Sesamum indicum L.) for drought tolerance. ► Chlorophyll a fluorescence, leaf temperature and stomatal conductance were evaluated. ► The performance index was more sensitive to drought stress than the quantum yield of photochemistry. ► Drought factor index (DFI) is proposed in this work to screen for improved drought tolerance. Drought is one of the major constraints limiting crop productivity in African Sahel. The aim of this study was to select mutant sesame (Sesamum indicum L.) lines with improved levels of drought resistance. Twenty-one M4-M5 sesame lines of unknown drought tolerance, and their three parental sources with well-known and contrasting drought tolerance levels were evaluated at the vegetative stage in a factorial pot experiment, using a completely randomized design with three replicates. After 2 weeks of growth, water was withheld for 16 days as drought stress treatment. Chlorophyll a fluorescence data, as well as stomatal conductance and flag leaf temperature were recorded during the stress period. Recorded chlorophyll a fluorescence transients were analyzed by the JIP-test to translate stress-induced damage in these transients to changes in biophysical parameters allowing quantification of the energy flow through the photosynthetic apparatus. Large genotypic differences in the extent to which drought stress affected chlorophyll a fluorescence transients were observed. Drought stress reduced the performance index and stomatal conductance, and increased flag leaf temperature but had little effect on maximum quantum yield of primary photochemistry. A drought factor index is proposed in this work to screen for improved drought tolerance in twenty-one M4-M5 sesame lines. Mutant lines shi165, lc162, mc112, lc164, icn115, icn141, mt169, dwf172 and cc102 exhibited drought factor index values superior to those of the known drought tolerant cultivars Birkan and 38-1-7. A significant and negative relationship was found between the drought factor index and the leaf temperature index. Finally, we succeeded in obtaining drought tolerant lines with good secondary traits by using mutagenesis and chlorophyll fluorescence technique.