The study sought to evaluate the effect of flexible working hours on employee performance of Isiolo County Government, Kenya. The study adopted a descriptive research design whereby quantitative data was collected using close-ended questionnaires. Therefore, the target population included 1,662 employees of Isiolo County government in various departments. These employees were further sampled using a simple random method to obtain 43 directors, 48 managers, and 309 operational staff as the sample size. Further, the study undertook a pre-test study in Samburu County government whose feedback was assessed using Cronbach Alpha coefficient to test the reliability of the questionnaires. SPSS software version 25 was used during the analysis process to provide descriptive and inferential analysis. The findings of the questionnaire indicated that 86(25%) respondents, strongly agreed and 117(35%) agreed on a mean of 4.21, that there is a local arrangement between the staff and their supervisors on how to deliver the assigned tasks on remote working option However, 76(22%) respondents, strongly disagreed and 107(32%) disagreed on a mean of 2.43, Tasks are sub-divided using a job-sharing technique to allow employees attend to other areas of their lives and still manage to attain the departmental objectives. The correlation coefficient for flexible working hours r=0.741 at α < 0.02 and 99% significance level. Flexible working hours had a positive effect on the performance of employees. It was established that there was a hybrid working method that included in-office and remote operations. That notwithstanding, the choice of hybrid options was based on an informal agreement between first-line supervisor and an employee. This brought about unprofessional favors and an unbalanced allocation of tasks to the staff. Consequently, the long-term effect was poor completion of tasks, late submission of assignments, and lack of adequate supervision leading to unsatisfactory work. The recommendations on flexible working hours are that there should be a formal policy structure formulation by the management that allows equality and fairness in allocation of tasks and the choice of either working in an office or remotely. Additionally, there should be empowerment of organization laws and regulations to support disciplinary actions by the management, to discourage late submission of assignments. There should be an encouragement of work contract signing an agreement between the workers and the supervisors that supports in job training to reduce work-related errors/ unsatisfactory work.