His father had previously converted to Methodism, and the young Aikins was educated at the Methodist-run Upper Canada Academy in Cobourg from 1840 to 1845.

Three years later, he was elected to the Province of Canada's legislature for the newly formed riding of Peel as a Clear Grit (i.e., radical reformer).

The Clear Grit faction in parliament had previously been aligned with Francis Hincks's governing Reformers, but this alliance ended after the 1854 election.

Aikins played only a minor role in the parliamentary debates on Canadian confederation, which he supported in principle despite concerns about the legislative means which John A. Macdonald was using to move the policy forward.

After Confederation was approved, Aikins attempted to introduce legislation for an elected senate, but was ruled out-of-order by the Council's speaker.

In 1868, Aikins was offered a cabinet position in Prime Minister John A. Macdonald's Liberal-Conservative government, but turned it down for fear of dividing the Liberal Party.

In this capacity, he oversaw various applications for government postings; he had little direct control over patronage in central Canada, but was a more powerful figure as regards the western provinces.

Aikins arrived in Manitoba during a period of discord between the provincial and federal governments; Macdonald had recently disallowed Premier John Norquay's railway legislation, and an opposition movement was forming around Thomas Greenway.

Aikins was under orders from Macdonald to ensure that provincial legislation reflected national policies, but his awkward relationship with Norquay made his task difficult.