At the 2019 CPL–U Sports Draft, Johnston was selected 10th overall by York United. In July 2020, he signed his first professional contract with York. 2021 was a breakout season for Johnston, as he became a regular starter, and was ranked the 27th best player in the Canadian Premier League at the end of the season. He was also nominated for the CPL Assist of the Year. Isaiah completed the 2024 season in the USL Championship with Loudoun United, where he made 14 appearances. Before joining Loudoun United, the 23-year-old dual-national (Canada/Jamaica) represented Huntsville City FC and York United FC.