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The Canterbury Health System has invested substantially in its transformation to a patient-centred, integrated system, enabling improved performance despite the significant and long-term impacts of the Christchurch earthquakes in 2010 and 2011. Questions have been raised about whether this transformation is sustainable and affordable. We argue that there is a need for a post-disaster health funding strategy that takes into account the challenge of following population movements after a large natural disaster, and higher costs resulting from the disruption and the effect on the population. Such a strategy should also provide stability in an unstable environment. However, funding for health in Canterbury has followed a 'business as usual' model using the population-based funding formula, which we view as problematic. Additionally, increases in funding using that formula have been below the national average, which we believe is perverse. Canterbury has received an additional $84 million government in deficit funding since 2010/11, and this has covered part of the extra cost attributable to the earthquake. However, without system-wide integration and innovation that was underway before, and that has continued since the earthquakes, it is likely the Canterbury Health System would not have been able to meet the health needs of its population. If health funding for Canterbury had continued to increase at the average rate applied across New Zealand over the past five years, deficit funding would not have been required.