On 21 September 2017, Brophy joined National League side Leyton Orient on a three-month loan deal until January 2018.[7] Two days later, he made his Orient debut during their 2–2 away draw with Aldershot Town, featuring for the entire 90 minutes.[8] On 24 November 2017, Brophy was recalled by parent club, Swindon, following increasing injury problems.[9] He rejoined Leyton Orient on a permanent basis on 31 January 2018, signing a 2+1⁄2-year deal.[10] Brophy was offered a new deal as his contract was due to be up at the end of June 2021 however he decided to turn down the offer to join Cambridge United F.C.[11] He left the club making 149 appearances.