Academic studies of gender pay gaps within higher education institutions have consistently found pay differences. However, theory on how organisation-level factors contribute to pay gaps is underdeveloped. Using a framework of relational inequalities and advanced quantitative analysis, this paper makes a case that gender pay gaps are based on organisation-level interpretations and associated management practices to reward ‘merit’ that perpetuate inequalities. Payroll data of academic staff within two UK Russell Group universities (N = 1,998 and 1,789) with seeming best-practice formal pay systems are analysed to determine causes of gender pay gaps. We find marked similarities between universities. Most of the variability is attributed to factors of job segregation and human capital, however we also delineate a set of demographic characteristics that, when combined, are highly rewarded without explanation. Based on our analysis of the recognition of ‘merit,’ we extend theoretical explanations of gender pay gap causes to incorporate organisation-level practices.