Lindsey Wilson College offers two Master of Education and one Master of Arts degrees. 

The School of Professional Counseling offers a degree in Counseling and Human Development with a specialization in mental health counseling.  This application-oriented program is designed to enhance the skills of bachelor-level practioners presently employed or planning a professional career in counseling.  In addition to offering the program on the AP White campus in Columbia, KY, the college offers the program in a week-end format through community-based programs in locations across Kentucky and in Ohio, Virginia and West Virginia.  The Master of Education in Counseling and Human Development is accredited by the Council for Accreditation of Counseling and Related Educational Programs (CACREP) standards.

The Division of Education offers the Master of Education degree Teacher as Leader.  The 30 hour degree program can be completed in two summers and one academic year, or adapted to meet the teacher's timeline for completion.  Graduates of the program will receive the Kentucky Teacher Leader endorsement and are eligible for Rank II status qualifying them to assume leadership career roles in their districts.  Course work is an integration of on-line sessions with eight on-campus meetings during the fall and spring semesters including selected courses delivered entirely on-line.  Close collaboration between graduate faculty and the local schools individualizes the program to the needs of the teacher, the students, and the school community allowing the teacher to integrate master's course work with teaching and leadership responsibilities.

Lindsey Wilson College also offers a Master of Arts in Christian Leadership. As an intentionally church - related college, the program's mission coincides with the stated purpose of the UMC Board of Higher Education which is to "develop the next generation of Christian leaders." The M.A. program is  broad and ecumenical, empowering graduates to become leaders in a  variety of church-related occupations. Employment opportunities exist within the local church as pastors, student ministry leaders or directors of Christian Education; in church extension ministries or parachurch organizations. Coursework is offered on the Columbia campus through an innovative delivery system of classes on Monday nights and weekend format. This enables working professionals to be fully employed while attending graduate school. For applicants with academic backgrounds in Christian Ministries, Christian Education or Religion, the degree may be completed in one intensive year.