There are three different kinds of ministry that the New York Divinity School is seeking to train and equip, and there is a Master’s-level Program designed for each. First, every Christian leader needs to engage Biblical insight and wisdom into daily life, in every workplace, and in every community. The Master's-Level Certificate of Arts in Faith and Practice equips all leaders for the levels of significance they desire. Second, every pastor, future pastor and chaplain should seek the full professional pastoral program, and the seminary offers that with the Master's-Level Certificate of Divinity Program. Third, Christian men and women may seek extensive knowledge of Christian behavior and belief, without the full professional pastoral program, or as a stepping stone to later upgrade to a professional program. The Master's-Level Certificate of Arts in Theological Studies (or "in Religion") will thoroughly serve their needs.

The Master's-level Certificate of Arts in Faith and Practice (48 hours including up to 12 hours transferred from another Master's Program) is designed for those professionals who have Master's-level professional training and work experience in their profession (such as government, law, business, medicine, education, accounting, engineering, social work or fine arts) and wish to engage a higher level of significance in their lives and in some aspect of work, profession, culture, or social/civic/economic issue in the light of Biblical and Christian teaching, to help equip them in their chosen field and Church leadership.

The educational objective of the Master's-level Certificate in Divinity Program (90-hours) is to prepare persons for the pastoral ministry in Christian churches. This Program is modeled after the standards used by most other seminaries, as well as denominations, chaplaincy requirements, and such like. This MDiv Program provides recognized professional training for men and women pursuing a calling into the pastorate or related ministry professions.

The Master's-level Certificate of Arts in Theological Studies (48 hours) and the equivalent Master's-level Certificate in Religion are the Program for men and women who are serious about the preparation and work of ministry, as pastors or lay people, although it is not the full MDiv professional Program. The MA in Religion Program provides Biblical, personal, historical, and theological training to equip people in ministry. Students who complete the MA in Religion Program and enter professional ministry will be encouraged to continue to further their training toward a Master's of Divinity Program. The MA in Religion is often chosen by those who plan further study toward a Doctor of Theology or a Doctor of Philosophy and a career in teaching in a university, a Christian school or a seminary.

Biblical ethos/ethics and Biblical apologetics/evangelism themes bind the curriculum together and penetrate all courses. The courses are organized into three main categories: (1) Bible-based Content, Understanding, and Application of Scripture; (2) Christ-centered Worldview/Theology, Conduct and Cogency; and (3) Spirit-led Personal Growth, Ministry Skills and Community Leadership.