Background/Objectives: Intrinsic biomarkers, such as serum vitamin D levels and the conjunctival ultraviolet autofluorescence (CUVAF) area, have been proposed to quantify sunlight exposure. Evidence suggests that reduced outdoor activity during the SARS-CoV-2 pandemic accelerated the progression of myopia; however, there is little information on the impact of such restrictions on vitamin D levels and CUVAF area in populations with myopia. This study aims to assess the association between serum vitamin D levels and conjunctival ultraviolet autofluorescence area (CUVAF) in young adults with myopia during and after the pandemic, as well as its relationship with sun exposure habits and the use of skin protection measures. Methods: A prospective observational study was carried out. A total of 59 students participated, 32 with a diagnosis of myopia and 27 controls, during SARS-CoV-2 pandemic. Two serological tests for total 25-hydroxy vitamin D (D2 + D3) (Calciferol) were taken, activity habits and sun exposure were identified using the Intermountain Live Well Institute tool, and CUVAF images were taken post-pandemic. Results: In the 59 participants, we observed similar vitamin D concentrations between the myopic and control groups during and after the pandemic. However, analysis of CUVAF areas after the pandemic revealed that myopes had significantly smaller areas compared to controls (p < 0.05). Conclusions: The study demonstrated that using vitamin D as a biomarker for outdoor activity requires additional investigation; the CUVAF biomarker showed a significant association with myopia.