Introduction: The COVID-19 pandemic disrupted research globally. How it impacted Canadian early-career health researchers (ECHRs) remains unclear. We administered a survey to understand the composition of ECHRs in Canada, their job experiences, and experiences of burnout during the COVID-19 pandemic. Methods: A cross-sectional survey was conducted in May 2023 of Canadian ECHRs defined as within 7 years of their first independent research position. Quantitative analyses included a description of respondents by research pillar, socio-demographic and workplace characteristics, and the prevalence of burnout, disengagement or exhaustion. Sample characteristics were compared to national data on ECHRs from a Canadian funding agency. Thematic analysis of free-text responses was also conducted. Results: A total of 225 respondents met the eligibility criteria. Most respondents were assistant professors and characteristics of our sample were like the national data. The COVID-19 pandemic posed many challenges to student recruitment, and emotional support of students, with over half of the respondents reporting a moderate to significant decline in mental health compared to pre-pandemic. A significant proportion of respondents were experiencing high burnout (62%, 95%CI:56-67%), exhaustion (64%, 95%CI: 57-70%) or disengagement (91%, 95%CI: 87-95%). Thematic analysis identified three themes: ongoing benefits/problems preceding the pandemic, unintended outcomes of strategies to manage/prevent/contain COVID-19, and reasons to stay in their current position. Conclusions: Our survey revealed that Canadian ECHRs reported many diverse challenges during the COVID-19 pandemic and high burnout, putting the sustainability of this workforce at risk. Improved systems are needed to understand the long-term impacts and support the future of the Canadian health research ecosystem.