Branhamism, like other Oneness groups, has historically favored baptism in the name of Jesus rather than the Trinitarian formula found in Matthew 28:19. This reflects Branhamism's denial of the Trinity and its affirmation of Jesus as the full manifestation of God. However, there is some variation within the Message movement on this point, with some groups practicing both formulations.

Branham's teaching suggests that the essential reality of baptism is entry into Jesus and alignment with his redemptive work and divine nature, regardless of the exact words used. The Matthew 28:19 formula is not rejected as inauthentic, but Branhamism interprets it through an Oneness lens: baptizing 'in the name of the Father and of the Son and of the Holy Spirit' is understood as baptizing into the one God known as Father, manifested as Son, and operative as Spirit. Some Branhamist congregations practice dual baptism formulas to accommodate both biblical texts.