On 3 January 2013, the Ministry of the Interior announced that President Ma Ying-jeou had approved the appointment of Yen to the position of Chief of the General Staff of the Republic of China Armed Forces.

The Executive Yuan officially appointed him on 8 August 2013 from his previous post as ROC Chief of the General Staff.

Acting Defense Minister Kao Kuang-chi replaces his position as the ROC Chief of the General Staff.

[5] Commenting on the recent abduction incident over a Taiwanese female in Sabah, Malaysia, Yen said that although the ROC Ministry of National Defense (MND) has the capability of special forces to save the woman, but then those armed forces are reserved for the use of armed conflict between nation, and MND should not step into an international incident which is the ROC Ministry of Foreign Affairs (MOFA) should do.

Overseas special forces deployment will only be possible if there is a mutual treaty between the ROC and the host country.