National Health Data Warehouses (NHDWHs) promise to improve individual and population health. These systems are now increasingly being deployed in low- and middle-income countries (LMICs), given increased recognition of the value of data analytics in informing decision-making. However, ethical issues relevant to implementation of NHDWHs in LMICs remain largely ignored or, at best, inadequately addressed. In this paper, we highlight and critically analyze several of the key ethical issues, including privacy, informed consent and trust, confidentiality and security, secondary data use, sustainability and implementation validity, risk-benefit ratio, governance and conflict of interest, justice, equity, access, and collaborative partnerships. We then provide a set of guiding principles and points to consider for countries and implementers to guide further decision-making around ethics of implementing NHDWHs within LMICs.