In July 2015, a national scheme for after-hours incentive funding for general practices was re-introduced in Australia, 2-years after funding was transferred to regional primary health care organisations (Medicare Locals). The re-introduction was recommended in a 2014 review of after-hours primary care reflecting the "overwhelming desire" among general practice. Given the centrality of after-hours care provision in rural and remote practices identified in the review, we compare and contrast the current and historical after-hours incentive funding mechanisms focussing on fairness towards rural general practices. While there are similarities between the current and historical mechanisms, significant differences exist. The comparison is not straightforward. The major consistency is utilisation of practice standardised whole patient equivalents (SWPE) as the basis of funding, inherently favouring large urban general practices. This bias is expected to increase given a shift in focus from practices with no option but to provide 24/7 care to any practice providing 24/7 care; and an associated increased funding per SWPE. Differences primarily pertain to classification processes, in which the realities of rural service provision and recognition of regional support mechanisms are given minimal consideration. Rapid introduction of the new general practice after-hours incentive funding mechanism has led to inconsistencies and has exacerbated inherent biases, particularly inequity towards rural providers. Impact on morale and service provision in non-urban areas should be monitored.