Fennel (Foeniculum vulgare Mill.) is a medicinal species which has not been examined as a ratoon crop. Ratooning lessens the production intensity, but the ratooned fennel seed yield and physiological processes may differ with stand age, irrigation regime, and genotype. Eleven fennel genotypes were, thus, subjected to either limited or sufficient water supply for 6 years. For each year, the crop was harvested in early autumn to measure seed yield, yield components, dry mass, and essential oil. Besides, some physiological characteristics relevant to seed yield were studied in certain years. Results indicated a biphasic behavior in seed and essential oil yields of the majority of genotypes with maximum seed yields (ranging from 2514 to 2635 kg ha −1 in different genotypes) being obtained from the well-watered plants mainly in the 4th year of harvest. Taking the period of 6 years and the two irrigation regimes together, genotypes Yazd, Kashan, and Shiraz showed a better productive performance. Meaningful positive associations were found between the seed yield and such yield components as seeds/plant and certain physiological attributes, i.e., proline and total soluble carbohydrates concentrations, water potential, relative water content, and superoxide dismutase, catalase, and ascorbate peroxidase activities. Maximum seed yields (ranging from 1605 to 1704 kg ha −1) and essential oil yields (ranging from 33.3 to 45.5 kg ha −1) of plants grown under water-limited conditions were found in genotypes that benefited more from osmoregulative and antioxidative roles of proline and the antioxidative enzymes (i.e., Shiraz, Yazd, and Kashan) and, hence, were able to withstand better against water limitation. Considering such physiological capabilities, agronomic performance, and minimum stand age effects, we discovered for the first time that certain fennel genotypes could be proposed as potential resources for growing fennel as an alternative ratooned crop for low production intensity and sustainable cropping in arid climates.