The author presents some analysis of HE governance in Mongolia in comparative framework. The presentation is devoted to University administration matters, particularly to relationship between Government and HEI, decision making regarding human resources, academic programs and research, setting tuition and fees. In highly competitive global context the key issues facing Mongolian Higher education are university autonomy, quality assurance, funding, program competitiveness and research effectiveness. Mongolian Government has approved National programs for development of outcome based HE system and research universities. Mongolian HEIs seeking more autonomy face strong challenges to cope with reduction of funding and accountability. Market oriented policies and demand to sustain a balance of teaching and research, urge HEIs to make a transition from traditional, politically motivated administration to corporate or shared governance models. The strengthening research links the industry and business without jeopardizing their academic integrity is main challenge for HEIs to make successful transition from traditional background of governance to more effective governance model. According to the author, transformative experiences and organizational developments of HEI in developed countries can be used successfully to guide actions towards positive catalyst change in Mongolian HE.