A budget is a basic and powerful tool in management and serves as a tool for planning and controlling the use of scare financial resources in the accomplishment of organizational goals. Most of the studies on budgeting mainly focused on challenges of budget preparation and utilization in the public sector.The study sought to determine the challenges of budget implementation in the public sector, a case of Meru County. The specific objectives were institutional constraints in budget implementation, performance in revenue collection, county government capacity on use of IFMIS and effective oversight and audit function. The study employed a descriptive research design. This study was a descriptive in nature done on a population consisting 80 members of staff who were in management positions in the thirteen (13) departments of Meru County and within the executive arm. These departments were Office of the Governor, County Treasury, Agriculture, water, education, health, planning, public service, transport, cooperatives, culture, public service board and town administration department.A sample was drawn from these targeted 80 employees in the county. A sample size of 40 comprised of ten (10) CECs,ten (10) COs and twenty (20) directors. Self -administered questionnaires were distributed to the sample drawn and descriptive analysis was employed. Pie charts, tables, graphs were then used as appropriate to present the data. The data was analyzed using multiple regressions. The ANOVA and model summary were used to measure the overall relationship between independent and dependent variables and the results showed that the probability of the F-statistic (29.455) for the overall regression relationship was greater than .001,less than the level of significance of 0.05. The multiple R for relationship between the set of independent variables and the dependent variables was 0.878 which means a very strong correlation. R2 which was 77.1% showed the proportion of the variation in the dependent variable that was expaained by the four independent variables. The study found out that the challenges of budget implementation in Meru County were related to institutional constraints, capacity on use of IFMIS and oversight and audit function. The study hence recommends a further research be done on another County and broaden the respondents to include both the middle level and top management. A further research could also be carried out on challenges of budget preparation in the public sector to see if the same results would be arrived at.