Extreme use of chemical fertilizers could reduce the quality of secondary metabolites in medicinal plants. Humic acid (HA) might benefit plant growth by improving nutrient uptake and hormonal effects. The main objective of this work was to study the effect of HA on yield of Silybum marianum (milk thistle) and Cucurbita pepo convar. pepo var. styriaca (medicinal pumpkin) seed and the seed oil characteristics. Different levels of HA (0, 500 and 1000 mg/L) were applied weekly on plants as foliar application one month after seed germination. The results showed that HA had no effect on yield of milk thistle and decreased pumpkin yield. HA treatment decreased oil content of both species. Regarding to oil quality, gas chromatography results indicated that oils unsaturation degree was improved by HA application. It could be concluded that although HA had no positive effect on yield and oil content, it was worthy in enhancement of nutritional value of the oils.