Despite the availability of skilled and high professionals' workers, there has been misallocation of human capital and there is a little benefiting from it is contribution to economic transformation. In this paper I attempt to investigate the reasons behind human capital misallocation and how lean productivity shapes today's Sudanese productive sectors. A theoretical analysis is considered to quantify the correlation relationships between human capital and economic transformation. Data from 2008-2014 labor force survey and National Statistics bureau survey are considered. Based on econometric time series data estimations over 2000-2014, we find evidence that human capital in Sudan is associated with lower productivity per worker and thereby lower economic growth. Results further show that labor market is characterized by a majority of workers are involved in unproductive and unpaid activities.