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Purpose Stock outs of cancer drugs are potentially fatal but have not been systematically studied in low- and middle-income countries. The aim of this study was to determine the availability and alignment of the Botswana National Essential Medicines List (NEML) for cancer drugs with the WHO's Essential Medicines List (EML). Methods The availability and cost of cancer drugs were analyzed using data from a weekly stock catalog sent by Botswana's Central Medical Store to all pharmacy departments in government hospitals. Comparative data were extracted from the WHO EML and the "International Drug Price Indicator Guide-2014" from the Management Sciences for Health. Interviews with key informants were used to collect data on the Botswana NEML and the drug supply chain in the public sector. Results The 2015 Botswana NEML for cancer had 80.5% alignment with the WHO EML. At least 40% of essential drugs were out of stock for a median duration of 30 days in 2015. Stock outs affected chemotherapy drugs included in first-line regimens for treating potentially curable diseases such as cervical, breast, and colorectal cancer and were not associated with buyer price of therapy. Analyses showed that the median price ratio for procured drugs was greater than 1 for 61% of the NEML drugs, which suggests inefficiency in procurement in the public sector. Conclusions Botswana has one of the highest alignments of NEML to the WHO EML in the sub-Saharan African region, which is consistent with investment in the health care system evident in other clinical spheres. Better quantification of chemotherapy requirements using data from the National Cancer Registry and resource-sensitive treatment guidelines can help reduce stock outs and facilitate more effective and efficient procurement processes.