First term
When the position of Premier was created in 1856, Stafford refused to compete for the office. Instead, it was taken by Sewell. Sewell's term, however, lasted only thirteen days, after which he was replaced by William Fox. Stafford refused offers of a ministerial position from both leaders. When Fox's government fell, having lasted exactly the same number of days as Sewell's, Stafford was deemed the only suitable candidate remaining, and agreed to become Premier. Stafford to date remains the youngest New Zealand Prime Minister on gaining office at 37 years, 5 weeks of age.
Among Stafford's first acts as Premier were measures to define the relationship between central and provincial government. Also notable was the unofficial establishment of Cabinet, which met independently of the official Executive Council. This meant that much government business was conducted without the presence of the Governor, straining relations between Governor Thomas Gore Browne and parliament.
Stafford also clashed with the Governor on the subject of the distribution of powers, particularly responsibility for dealings with Māori. Thomas Gore Browne, disdainful of the chaotic nature of the Sewell and Fox premierships, did not believe that parliament should have control over such an important matter, while Stafford pursued his old goal of democratic self-government. Stafford, on behalf of the new government, refused all responsibility for financing actions undertaken by the governor without parliament's approval.
In 1858 and 1859, Stafford was out of New Zealand, attempting to negotiate on the country's behalf for various services. His trip proved problematic, however – during his absence, his colleagues and Governor Browne agreed to force Māori into selling land at Waitara, despite Stafford's strong objections. Forcing Māori to sell their land triggered the First Taranaki War. Stafford condemned the decision on grounds of both economics and morality and considered resignation. Eventually, he chose to continue his premiership, but Stafford's views on relations with the Māori were eventually to cause his departure regardless – attacks by William Fox on Stafford's "weakness", and Stafford's lack of support for the Invasion of the Waikato, caused him to lose parliament's confidence by a single vote in July 1861. William Fox became Premier once again.
When Fox's government fell one year later, Stafford had the opportunity to become Premier again, but declined. His stated reason for doing so was his hostility to Governor George Grey, whom Stafford believed he would be unable to override on policy matters – Stafford did not wish to become Premier if the Governor would simply block his policies. Instead, Alfred Domett took the premiership. Domett's premiership has been described as "like a Stafford ministry without Stafford", although the invasion of the Waikato began in July 1863. Domett was replaced by Frederick Whitaker after little more than a year, but Whitaker himself only lasted a similar time before being replaced by Frederick Weld. Weld, like Domett, followed policies similar to Stafford, although did not enjoy good personal relations with him.
