Naughten was appointed as Minister for Communications, Climate Action and Environment in Taoiseach Enda Kenny's Fine Gael/Independent minority government after two months of negotiation following the 2016 general election. He later resigned from this post on 11 October 2018, following controversy surrounding a series of meetings he attended with the leading bidder for his department's National Broadband Plan that occurred during the project's procurement process. He was replaced by Richard Bruton. He stood for election for Ceann Comhairle at the first sitting of the 33rd Dáil on 20 February 2020, but was defeated by Seán Ó Fearghaíl. Naughten was subsequently appointed by Leo Varadkar as the Leas-Cheann Comhairle on an acting basis due to a deferred election caused by the COVID-19 pandemic.