County governments in Kenya have been consistently accused of poor budget absorption. However, there are no comprehensive studies that have been advanced to assess the challenges cited by the office of controller of budget on absorption rates in county governments. This study sought to assess the challenges affecting budget absorption in the county governments. The study specifically sought to assess the delays in disbursement of funds from national government, manpower capacity, delays in procurement process and capacity of oversight committee members’ on budget absorption in County Governments. Descriptive research design was used to conduct the research in Nakuru, Nyandarua and Laikipia Counties. The target population for the study was 270 comprising of 69 directors and 201 heads of departments. The sample size comprised of 18 directors and 55 department heads.  Data collection was done using self-administered questionnaires administered using the drop and pick later method. Data analysis was done using means, mode and standard deviations frequencies and percentages. In addition, chi square analysis and multiple linear regression analysis were used to determine the extent to which the challenges affect budget absorption. Data was then presented in Tables, graphs and charts for easy interpretation and discussion. The study found out that there were delays in disbursement of funds from the national governments to county treasuries and from the county treasuries to various department projects and activities. Further, procurement functions in the county governments were inefficient owing to the lead time and bureaucracies involved in procurement. Although budget oversight committees were present they were inefficient and compromised in conducting their jobs. However these factors did not significantly contributed to the low levels of budget absorption since they only accounted for 6.0%. The study therefore recommended for county governments in collaboration with commission for revenue allocation and the national treasuries to come up with a criterion for ensuring smooth flow of funds from the national treasury to the end user departments. There is need for both the county government and the national government to relook at the current procurement laws which are bureaucratic and influence budget absorption.