This thesis sought to deepen the understanding of the Desert of Loneliness through the study of the lived-experience of Sr. Mary Joseph of the Infant Jesus, Foundress of the Franciscan Missionary Sisters of the Infant Jesus, from the vantage point of the Franciscan Spirituality. It aims to help the sisters of the Congregation and other readers to have a wider knowledge of the historical context and events in the life of the Foundress, providing an in-depth understanding of her lived-experience of the Desert of Loneliness and how she faced it. The study hopes to help the readers handle their own experience of the Desert of Loneliness creatively. This research dealt with the excruciating pain of the Desert of Loneliness taken from the writings of the Foundress and documents of the Congregation. It identified the Desert of Loneliness as the subject of the study based on the typologies of loneliness according to Edward Wakin and Sean Cooney, Malka Margalit, and James Park. The author focused on the following types of loneliness: emotional loneliness, social loneliness, cultural loneliness, cosmic loneliness, existential loneliness, representational loneliness, and spiritual loneliness. Sr. Mary Joseph was able to overcome her Desert of Loneliness because of her deep connection to the LORD. Her Franciscan Spirituality played an important role in her experience.