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Background  Spatial and temporal malaria risk maps are essential tools to monitor the impact of control, evaluate priority areas to reorient intervention approaches and investments in malaria endemic countries. Here, the analysis of 36 years data on  Plasmodium falciparum  prevalence is used to understand the past and chart a future for malaria control in Kenya by confidently highlighting areas within important policy relevant thresholds to allow either the revision of malaria strategies to those that support pre-elimination or those that require additional control efforts.    Methods   Plasmodium falciparum  parasite prevalence ( Pf PR) surveys undertaken in Kenya between 1980 and 2015 were assembled. A spatio-temporal geostatistical model was fitted to predict annual malaria risk for children aged 2–10 years ( Pf PR 2–10 ) at 1 × 1 km spatial resolution from 1990 to 2015. Changing  Pf PR 2–10  was compared against plausible explanatory variables. The fitted model was used to categorize areas with varying degrees of prediction probability for two important policy thresholds  Pf PR 2–10  < 1% (non-exceedance probability) or ≥ 30% (exceedance probability).    Results  5020 surveys at 3701 communities were assembled. Nationally, there was an 88% reduction in the mean modelled  Pf PR 2–10  from 21.2% (ICR: 13.8–32.1%) in 1990 to 2.6% (ICR: 1.8–3.9%) in 2015. The most significant decline began in 2003. Declining prevalence was not equal across the country and did not directly coincide with scaled vector control coverage or changing therapeutics. Over the period 2013–2015, of Kenya’s 47 counties, 23 had an average  Pf PR 2–10  of < 1%; four counties remained ≥ 30%. Using a metric of 80% probability, 8.5% of Kenya’s 2015 population live in areas with  Pf PR 2–10  ≥ 30%; while 61% live in areas where  Pf PR 2–10  is < 1%.    Conclusions  Kenya has made substantial progress in reducing the prevalence of malaria over the last 26 years. Areas today confidently and consistently with < 1% prevalence require a revised approach to control and a possible consideration of strategies that support pre-elimination. Conversely, there remains several intractable areas where current levels and approaches to control might be inadequate. The modelling approaches presented here allow the Ministry of Health opportunities to consider data-driven model certainty in defining their future spatial targeting of resources.    Electronic supplementary material  The online version of this article (10.1186/s12936-018-2489-9) contains supplementary material, which is available to authorized users.

Spatio-temporal analysis of Plasmodium falciparum prevalence to understand the past and chart the future of malaria control in Kenya