A number of baby wipe formulations contain 2-phenoxyethanol (PE) as a preservative and cetylpyridinium chloride (CPC) as a surfactant with antimicrobial activity. Previously, we reported the skin absorption of PE in porcine skin and human skin in vitro. In the present work, the permeation of PE from preparations with CPC and without CPC was investigated in human skin in vivo. The studies were conducted using Confocal Raman Spectroscopy (CRS) and tape stripping (TS) methods. The CRS studies showed that the area under the curve (AUC) of PE for the formulation with and without CPC were not significantly different (p > 0.05). The TS data indicated no significant difference in the amounts of PE recovered from tapes 1–6 for the preparation with and without CPC (p > 0.05). When comparing the in vitro and in vivo data, a correlation was observed between the cumulative amount of PE permeated through human skin in vitro at 24 h and the AUC as measured by CRS (r2 = 0.97). In addition, the cumulative amount of PE permeated through human skin in vitro at 24 h was found to correlate with the amount of PE recovered from tape 1 to 6 in vivo (r2 = 0.95). Both CRS and TS techniques demonstrated limitations in assessing the distribution of PE and CPC in the skin in vivo, primarily attributed to the Raman signal intensities of compounds under investigation and the variability in the amount of SC collected by TS. Despite the limitations of CRS and TS, the results from the present study add further insights to the in vitro permeation data. Additionally, the findings of the present study encourage the further development and application of CRS for non-invasive evaluation of topical skin formulations in vivo.