Background: Alopecia areata (AA) is a common autoimmune disorder characterized by patchy hair loss. There are many treatments available for AA. However, treatments of severe forms of AA are not satisfactory. Recently, oral Janus kinase (JAK) inhibitors were found to be effective for the treatment of severe AA variants. Objective: The aim of this work was to evaluate and compare the efficacy, side effects, and durability of two oral JAK inhibitor medications (ruxolitinib and tofacitinib) in the treatment of severe AA. Methods: This study included 75 patients with AA with more than 30% scalp hair loss, alopecia totalis, and alopecia universalis randomized into 2 groups. The first group (n = 38) received ruxolitinib 20 mg twice daily, and the second group (n = 37) received oral tofacitinib 5 mg twice daily. The treatment continued for 6 months followed by 3 months of follow-up off therapy. Efficacy of treatment was assessed by monitoring the change in the Severity of Alopecia Tool (SALT) score. Results: Both tofacitinib and ruxolitinib induced remarkable hair regrowth, with a mean change in SALT score of 93.8 ± 3.25 in the ruxolitinib group and 95.2 ± 2.69 in the tofacitinib group. However, the ruxolitinib group showed a shorter duration for initial hair regrowth. There was no statistically significant difference between the groups regarding hair regrowth at the end of the 6-month treatment and relapse rate at the end of the 3-month follow-up. Around two thirds of cases experienced relapse. Both drugs were well tolerated, with no reported serious adverse effects. Conclusion: Both ruxolitinib and tofacitinib could be considered effective and well-tolerated treatments for extensive AA.