Background: Wound healing includes processes such as cell migration, extracellular matrix deposition, remodeling, and angiogenesis. In addition, antioxidative and anti-inflammatory reactions play key roles in the process of wound healing. Previous studies showed that Linum usitatissimum (LU) had anti-inflammatory, antimicrobial, and antioxidant activities. LU also stimulates fibroblast proliferation in the skin tissue. Objectives: Herein, we studied the effects of topical LU on the wound healing process in rat models, according to histomorphometrical and stereological parameters. Methods: In this experimental study, 48 male rats (Wistar; 200 ± 20 grams) were randomly separated into four groups (n = 12): 5% LU gel-treated (E1), 10% LU gel-treated (E2), gel base-treated (C2), and the control group (C1), which received no treatment. A full thickness circular wound was created on the neck in each rat. At the end, the stereological evaluations, including wound closure rate, collagen, vascular and hair follicle density estimation, fibroblast proliferation, vascular length density, and mean diameter were performed. The data was analyzed, and P < 0.05 was considered statistically significant. Results: The average of the wound areas, collagen bundle synthesis, vascularization, and hair follicles in the LU-treated groups were significantly higher than the control group (P < 0.05). According to the estimated parameters, the contrast between E1 and E2 was insignificant. Conclusions: Overall, topical LU showed the potential to enhance the wound healing process and tissue regeneration. However, more studies, particularly clinical trials, are highly recommended on LU and its mixture with other healing agents to find more potent treatments.