This study focuses mainly on investigating differences in Southern and Northern general contractors’ perception of challenges in executing green building projects. The questionnaire survey-based data analysis results show that there is a good consensus between general contractors (GCs) from these two regions on the top two most critical challenges in delivering green building projects. They are “lacking of legal regulations and technical codes on green building”, and “more difficult to early establish a competent, integrated, and multidisciplinary green building project team”. Additionally, the Mann-Whitney U-test reveals that there are a significant difference on perception of the GCs from Northern as compared with those from Southern on the five challenges, including “shortage of reliable green building materials, technologies, and equipment in the market”, “lack of reliable suppliers of green products, materials, equipment”, “lack of appropriate tools/laboratories specific for testing, assessing, measuring, and inspecting the green performance of construction products”, “difficulty in selecting and managing subcontractors”, and “difficult in comprehending the green specifications”. The study may be beneficial not only for the central policymakers but also for the local governments, industrial practitioners and project stakeholders to gain a better understanding of the major challenges in executing green building projects at local or regional level. As a result, the study proposed many solutions specific for each of these regions to promote the development of the local green building industry.