* New-Englands Plantation (1630)
* The Cause of God and His People in New-England (1663)
* The Deplorable State of New-England (1662)
* The Works of John Higginson (2 vols., 1971-1973)
Sermons
* A Farewell Sermon (1663)
* A Sermon Preached at the Ordination of Mr. Samuel Willard (1670)
* A Sermon Preached at the Ordination of Mr. Increase Mather (1684)
* A Sermon Preached at the Ordination of Mr. Cotton Mather (1685)
Other Writings
* A Letter to the Church of Christ at Charlestown (1669)
* A Reply to the Answer of the Elders of the Churches of New-England (1664)
* A Vindication of the New-England Churches (1669)