Member missions are missionary agencies that have become members of JEMA. All their missionaries automatically become JEMA members and the missions have voting rights at JEMA meetings.
- Association of Baptists for World Evangelism (ABWE)
- Agape Mission (AGAPE)
- American Baptist Foreign Mission Society (ABFMS)
- Asian Access (A2)
- Assemblies of God Missionary Fellowship (AGMF-USA)
- Christian Reformed Japan Mission (CRJM)
- Church Missionary Society – Australia (CMS)
- Church of God Mission (CG)
- Converge Japan (CJ)
- Evangelical Covenant Church (ECC)
- Evangelical East Asia Mission (EEAM)
- Evangelical Free Church of America ReachGlobal Japan (EFCA RGJ)
- Evangelical Free Church of Canada ServeBeyond (EFCC SB)
- Finnish Lutheran Mission (FLM)
- German Alliance Mission (GAM)
- International Mission Board (IMB/SBC)
- International Ministerial Fellowship (IMF)
- JVENTURE
- Japan Campus Crusade for Christ (JCCC)
- Japan Christian Link (JCL)
- Japanese Evangelical Missionary Society (JEMS)
- Japan Fellowship Deaconry Mission (JFDM)
- Japan Free Will Baptist Mission (JFWBM)
- Japan Lutheran Brethren Mission (LBIM)
- Japan Presbyterian Mission (Mission to the World) (JPM-PCA)
- Liebenzell Mission International (LMI)
- Lutheran Evangelical Association of Finland (LEAF)
- Lutheran Free Church of Norway, Japan Mission (ELFCN)
- Multiply
- New Life Ministries (NLMS)
- North American Baptist General Mission in Japan (NAB)
- Norwegian Lutheran Mission (NLM)
- OMF International (OMF)
- OMS Christian Mission Church (OMS)
- Pioneers
- Reaching Japan Together Association/Reaching Japan Together (RJTA/RJT)
- SEND International (SEND)
- Serge
- The Christian and Missionary Alliance, Japan Mission (C&MA)
- The Evangelical Alliance Mission (TEAM)
- The Navigators (NAVS)
- The Redeemed Christian Church of God (RCCG)
- WEC International (Worldwide Evangelization for Christ International) (WEC)
- Wesleyan Mission in Japan (WM)
- Word of Life Japan
- World Gospel Mission (WGM)