ObjectivesTo identify differences in average basic pay between groups of National Health Service (NHS) doctors cross-classified by ethnicity and gender. Analyse the extent to which characteristics (grade, specialty, age, hours, etc.) can explain these differences.DesignRetrospective observational study using repeated cross-section design.SettingHospital and Community Health Service (HCHS) in England.ParticipantsAll HCHS doctors in England employed by the NHS between 2016 and 2020 appearing in the Digital Electronic Staff Record dataset (average N=99 953 per year).Main outcome measuresHours-adjusted full-time equivalent pay gaps; given as raw data and further adjusted for demographic, job, and workplace characteristics (such as grade, specialty, age, whether British nationality, region) using multivariable regression and statistical decomposition techniques.ResultsPay gaps relative to white men vary with the ethnicity-gender combination. Indian men slightly out-earn white men and Bangladeshi women have a 40% pay gap. In most cases, pay gaps can largely be explained by characteristics that can be measured, especially grade, with the extent varying by specific ethnicity-gender group. However, a portion of pay gaps cannot be explained by characteristics that can be measured.ConclusionsThis study presents new evidence on ethnicity-gender pay gaps among NHS doctors in England using high quality administrative and payroll data. The findings indicate all ethnicity-gender groups earn less than white men on average, except for Indian men. In some cases, these differences cannot be explained giving rise to discussions about the role of discrimination.