The Mar Thoma Youth Fellowship serves as a vital ministry dedicated to the spiritual formation, fellowship, and empowerment of the younger generation within the church. Designed primarily for high school students, college students, and young professionals, the Youth Fellowship operates with the core mission of helping young people build a personal, enduring relationship with Jesus Christ and understand their unique identity as Mar Thomites. Operating as a contemporary, largely English-speaking branch of the church's youth ministries, it ensures that young members are equipped with a strong biblical foundation, moral clarity, and the leadership skills needed to shape the church's future.

In Canada, local groups like the Canadian Mar Thoma Church (CMTC) Youth Fellowship operate under the Diocese of North America and Europe to specifically serve youth raised in the diaspora. Recognizing the distinct challenges of growing up as second- and third-generation immigrants, the Fellowship acts as a crucial cultural and spiritual bridge. It tailors the rich traditions and Eastern Reformed theology of the Mar Thoma Church so that they resonate deeply within a Western context. By doing so, it creates a safe, supportive space for Indo-Canadian youth to ask complex questions about their faith, navigate real-world academic and social pressures, and build lifelong peer support networks.

The Youth Fellowship serves as an energetic hub within the local parish, driving a dynamic calendar of spiritual and community events. Regular gatherings typically feature contemporary praise and worship, interactive Bible studies, and open discussions on applying Christian values to modern challenges. Beyond these weekly or biweekly routines, the Fellowship organizes major annual initiatives such as weekend lock-ins, regional retreats, diocesan-level Youth Conferences, and the dedicated Youth Sunday, during which members actively lead the English parish worship service. Committed to putting faith into action, the youth also lead various outreach and charitable efforts—ranging from volunteering at local Canadian food banks and homeless shelters to raising funds for global mission projects.