These data is part of the nationwide testing of SARS-CoV-2 at the KEMRI-Wellcome Trust Programme, Kenya. It contains results of specimens collected between in June 2020 which were processed and screened for SARS-COV-2 using real-time polymerase chain reaction (RT-PCR). Aside from that, it also contains the quantification cycle (Ct) values for both the pools and the individual Ct values. The data is used to describe the experience of using pooled testing at KEMRI-Wellcome Trust Programme, Kenya.