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<h4>Background</h4>Availability of essential medicines for non-communicable diseases (NCDs) is poor in low- and middle-income countries. Availability and cost are conventionally assessed using cross-sectional data. However, these characteristics may vary over time.<h4>Methods</h4>We carried out a prospective, descriptive analysis of the availability and cost of essential medicines in 23 Ugandan health facilities over a five-week period. We surveyed facility pharmacies in-person up to five times, recording availability and cost of 19 essential medicines for NCDs and four essential medicines for communicable diseases.<h4>Results</h4>Availability of medicines varied substantially over time, especially among public facilities. Among private-for-profit facilities, the cost of the same medicine varied from week to week. Private-not-for-profit facilities experienced less dramatic fluctuations in price.<h4>Conclusions</h4>We conclude that there is a need for standardized, continuous monitoring to better characterize the availability and cost of essential medicines, understand demand for these medicines, and reduce uncertainty for patients.