There is increasing pressure for reduction of user fees, but this can have adverse effects by decreasing facility-level funds. To address this, direct facility funding (DFF) was piloted in Coast Province, Kenya, with health facility committees (HFCs) responsible for managing the funds. We evaluated the implementation and perceived impact 2.5 years after DFF introduction. Quantitative data collection at 30 public health centres and dispensaries included a structured interview with the in-charge, record reviews and exit interviews. In addition, in-depth interviews were conducted with the in-charge and HFC members at 12 facilities, and with district staff and other stakeholders. DFF procedures were well established: HFCs met regularly and accounting procedures were broadly followed. DFF made an important contribution to facility cash income, accounting for 47% in health centres and 62% in dispensaries. The main items of expenditure were wages for support staff (32%), travel (21%), and construction and maintenance (18%). DFF was perceived to have a highly positive impact through funding support staff such as cleaners and patient attendants, outreach activities, renovations, patient referrals and increasing HFC activity. This was perceived to have improved health worker motivation, utilization and quality of care. A number of problems were identified. HFC training was reportedly inadequate, and no DFF documentation was available at facility level, leading to confusion. Charging user fees above those specified in the national policy remained common, and understanding of DFF among the broader community was very limited. Finally, relationships between HFCs and health workers were sometimes characterized by mistrust and resentment. Relatively small increases in funding may significantly affect facility performance when the funds are managed at the periphery. Kenya plans to scale up DFF nationwide. Our findings indicate this is warranted, but should include improved training and documentation, greater emphasis on community engagement, and insistence on user fee adherence.