Health systems reform processes have increasingly recognized the essential contribution of communities to the success of health programs and development activities in general. Here we examine the experience from Kilifi district in Kenya of implementing annual health sector planning guidelines that included community participation in problem identification, priority setting, and planning. We describe challenges in the implementation of national planning guidelines, how these were met, and how they influenced final plans and budgets. The broad-based community engagement envisaged in the guidelines did not take place due to the delay in roll out of the Ministry of Health-trained community health workers. Instead, community engagement was conducted through facility management committees, though in a minority of facilities, even such committees were not involved. Some overlap was found in the priorities highlighted by facility staff, committee members and national indicators, but there were also many additional issues raised by committee members and not by other groups. The engagement of the community through committees influenced target and priority setting, but the emphasis on national health indicators left many local priorities unaddressed by the final work plans. Moreover, it appears that the final impact on budgets allocated at district and facility level was limited. The experience in Kilifi highlights the feasibility of engaging the community in the health planning process, and the challenges of ensuring that this engagement feeds into consolidated plans and future implementation.