Background In refugee settings, safe and private access to sanitation is often constrained by overcrowding and limited infrastructure. While coverage indicators such as toilet availability are often used to monitor progress, they do not capture users lived experiences. The Sanitation-related Quality of Life (SanQoL-5) index measures individual sanitation experiences across five dimensions: privacy, safety, disgust, shame, and disease risk. This study assessed sanitation access and SanQoL-5 among refugee populations in Gambella, Ethiopia, and identify factors associated with variation in SanQoL-5.Methods We conducted a cross-sectional, representative survey across two refugee settlements in Gambella, Ethiopia, a region hosting approximately 42% of the country's total refugee population. Data were collected on sanitation access, facility type, location and characteristics, alongside experiential outcomes using SanQoL-5 (scored 0–1; higher scores indicate better quality of life). Generalised linear regression models were used to explore associations between SanQoL-5 scores, and hypothesised factors, including gender, facility type and location, construction quality, and cleaning arrangements. Analyses were stratified by toilet location (on- or off-compound) following evidence of effect modification.Results 764 respondents participated, of whom 307 (40%) reported access to a sanitation facility. Among toilet users, 36% (n = 110) used pit latrines and 64% (n = 197) urine-diverting dry toilets (UDDTs). The remaining 457 (60%) respondents reported practising open defecation (OD). Mean SanQoL-5 scores were higher among toilet users (SanQoL-5 0.60, 95% CI: 0.58–0.62) than those practising OD (SanQoL-5: 0.25, 95% CI: 0.23–0.28). Toilet location emerged as a determinant of SanQoL-5, with higher scores observed for toilets located outside household compounds. Among toilets located within compounds, users of pit latrines reported slightly higher SanQoL-5 scores than users of UDDTs (β = 0.04, p = 0.057), while no such differences were observed for toilets located outside compounds. Female respondents consistently reported lower SanQoL-5 scores than males regardless of toilet access, type, or location.Conclusions Sanitation coverage was low, with 60% of respondents reporting no access to a sanitation facility. SanQoL-5 varied widely by toilet access, toilet location, and gender, while sanitation facility type played a more limited role, illustrating the value of measuring experiences as well as infrastructure. This study represents the first application of SanQoL-5 in a humanitarian setting, demonstrating its feasibility and utility in refugee populations. From an operational perspective, improving access to sanitation and optimising toilet location may yield greater gains in user experience than facility type alone in refugee settings.