BackgroundKenya grapples with a paradox; severe public sector workforce shortages co-exist with rising unemployment among healthcare professionals. Medical schools have increased trainee outputs, but only 45% of newly qualified/registered doctors were absorbed by the public sector during 2015–2018. In such a context, we explore what influences doctors’ career choices at labour market entry, specifically understanding the role of public service motivation (PSM).MethodsWe conducted a cross-sectional and prospective study of interns and recently graduated doctors to examine PSM, their intention to work in the public sector and their final employment sector and status. We surveyed them on their PSM and job intentions and conducted a prospective follow-up survey of the interns, around one year later, to understand their employment status.FindingsWe recruited 356 baseline participants and followed up 76 out of 129 eligible interns. The overall PSM score was high among all participants (rated 4.50/5.00) irrespective of sector preferences. 48% (171/356) of the participants preferred to work in the public sector immediately after internship, alongside 16% (57/356) preferring direct entry into specialist training—commonly in the public sector. Only 13% (46/356) and 7% (25/365) preferred to work in the private or faith-based sector. Despite the high proportion of interns preferring public sector jobs, only 17% (13/76) were employed in the public sector at follow-up and 13% (10/76) were unemployed, due to lack of job availability.ConclusionHigh PSM scores irrespective of sector preferences suggest that doctors are generally committed to serving the ‘public good’. Many intended to work in the public sector but were unable to due to lack of job opportunities. Policymakers have an opportunity to tackle workforce gaps in the public sector as young doctors continue to express a preference for such work. To do this they should prioritise creating adequate and sustainable job opportunities.