Background More than four million child deaths occur annually; most are neither adequately documented nor investigated. The Child Health and Mortality Prevention Surveillance (CHAMPS) program was launched in Sierra Leone (SL) to generate high-quality data to determine definitive causes of stillbirths and under-five mortality (U5M) to inform decision-makers. Despite the multiple challenges of a greenfield research site, we highlight the experience of setting up a high-quality mortality surveillance (MS) system, including the viability of Minimal Invasive Tissue Sampling (MITS). Methods To establish the MS program, we implemented qualitative research and community entry, a sensitive system for timely identification and notification of deaths and followed CHAMPS standard operating procedures for investigating deaths and assigning accurate and definitive causes of death. CHAMPS in SL was implemented in four phases during 2017-2019 by a consortium. Enrolled stillbirths and U5M underwent verbal autopsy, clinical-data-abstractions, MITS, microbiology, molecular and histopathological diagnoses, and Determination of Cause of Death (DeCoDe). Results CHAMPS achieved a 93% consent rate, capitalizing on existing Ministry of Health infrastructure, community involvement, and local ownership. As of December 2022, 3,433 deaths were registered, with 1,056 (31%) eligible for enrolment. Of 439 cases DeCoDed, 402 (92%) of case-families had received feedback on the cause of death. Using findings and recommendations from the DeCoDe experts, CHAMPS is implementing interventions to reduce stillbirths and U5M at CHAMPS SL, including clinical review meetings, provision of emergency drugs and routine child death audits. Conclusion Implementing innovative MS in a challenging context, such as SL, is possible. Building on local knowledge and infrastructure has enabled the CHAMPS project to achieve remarkably high consent rates, given the cultural, religious and sensitivity challenges surrounding seeking consent for MITS from caregivers who have just lost a child. The programme has invested significantly in upscaling local technical capacity for surveillance and laboratory diagnostics.