Chronic pain encompasses a range of painful conditions such as migraines, fibromyalgia, or prolonged periods of pain without a specific etiological cause. In this context, a less complex, easily applicable therapy that reduces side effects and does not require a high investment from the patient becomes highly important. Currently, chronic pain treatment with topically applied endocannabinoids has been a subject of research. However, permeation studies are necessary to ensure efficacy, safety, and delivery of the active ingredient to the skin layers. Confocal Raman Spectroscopy (CRS) has emerged as an analytical method for the analysis of materials, including biological tissues. In this context, the present study brings an in vivo approach using Confocal Raman Spectroscopy to analyze in vivo the permeation of two formulations containing Cannabidiol (CBD). One formulation consists of nanoencapsulated CBD in transferosomes (TRANS), while the other is a nanolipid carrier containing nanoencapsulated CBD in transferosomes (CLN TRANS). The aim of this study is to explore the topical treatment of chronic pain using these formulations and assess their permeation characteristics. Raman data were collected from stratum corneum, epidermis and dermis at T0, T4 and T8h after topical application. It was possible to identify that both products showed to permeate to the dermis, but with different kinetics.