Neill was strongly opposed to Brexit prior to the 2016 referendum. On 7 February 2017, along with six other Conservative Members of Parliament, he defied the Party whip and voted in favour of New Clause 110 of the European Union (Withdrawal) Bill. In December 2017, in the same bill, he voted along with fellow Conservative Dominic Grieve and nine other Tory MPs against the government, and in favour of guaranteeing Parliament a "meaningful vote" on any deal Theresa May agrees with Brussels over Brexit.