He saved the Southern Baptist Theological Seminary financially in the 1870s. There is now an endowed chair, the Joseph Emerson Brown Chair of Christian Theology, at the institution. Brown and his wife, Elizabeth Grisham Brown, were honored in 1928 by a statue installed on the state capitol grounds. In 2020, the Southern Baptist Theological Seminary vacated the Joseph Emerson Brown chair of theology because the seminary felt, according to President Albert Mohler, that the name was "wrongly commemorated" by the Seminary due to Brown's position on slavery.