Yes, according to at least one hadith, the Prophet Muhammad (PBUH) used henna.
The following provides more detail:
- A hadith narrated by Aisha (may Allah be pleased with her) in Sahih al-Bukhari states that the Prophet Muhammad (PBUH) "used to have his hair dyed with henna and then perfume it with musk." This hadith is considered authentic.
Therefore, based on this hadith, the Prophet (PBUH) did use henna.