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Abstract Background Little is known about the state of mental health systems in Kenya. In 2010, Kenya promulgated a new constitution, which devolved national government and the national health system to 47 counties including Kilifi County. There is need to provide evidence from mental health systems research to identify priority areas in Kilifi’s mental health system for informing county health sector decision making. We conducted an initial assessment of state of mental health systems in Kilifi County and documented resources, policy and legislation and spectrum of mental, neurological and substance use disorders. Methods This was a pilot study that used the brief version of the World Health Organization’s Assessment Instrument for Mental Health Systems Version 2.2 to collect data. Data collection was based on the year 2014. Results Kilifi county has two public psychiatric outpatient units that are part of general hospitals. There is no standalone mental hospital in Kilifi. There are no inpatients or community based facilities for people with mental health problems. Although the psychiatric facilities in Kilifi have an essential drugs list, supply of drugs is erratic with frequent shortages. There is no psychiatrist or psychologist in Kilifi with only two psychiatric nurses for a population of approximately 1.2 million people. Schizophrenia was the commonest reason for visiting outpatient facilities (47.1%) while suicidal ideation was the least common (0.4%). Kenya’s mental health policy, which is being used by Kilifi County, is outdated and does not cater for the current mental health needs of Kilifi. There is no specific legislation to protect the rights of people with mental health problems. No budget exists specifically for mental health care. There have been no efforts to integrate mental health care into primary care in Kilifi, and there is no empirical research work to evaluate its feasibility. Conclusion There is an urgent need to increase resources allocated for mental health in particular infrastructure and human resource. Policy and legislations need to be established to protect the rights of people with mental illnesses, and mental health should be integrated with primary care to increase access to services.