Gantogtokh began his career with Mongolian club Arvis FC at age nine. He remained with the club until 2019 when his parents decided to relocate to the Czech Republic. Upon arriving in the country, he joined local side FK Meteor Tábor. For the 2021–22 season, he was promoted to the club's reserve team.[1] He was called the "discovery of the season" by his head coach after scoring five goals in seven matches after joining the side.[2] One of his goals was the game-winner against SK Ratibořské Hory in September 2021. With the win, the team sat at the top of the table.[3] The team went on to win the league that season with Gantogtokh as the league's top scorer with forty-five goals in twenty-four matches.[4]
In summer 2022, Czech First League club SK Dynamo České Budějovice took note of Gantogtokh's performance with Tábor and invited the player to join its academy after an impressive trial.[5] On 6 September 2023, he made his first appearance for the first team, coming on as a second-half substitute for Patrik Hellebrand in a friendly against Austrian club LASK Linz.[1][6] He made his competitive league debut for the first team on 11 November 2023. He entered as an 82nd-minute substitute in the eventual 0–1 defeat to FK Teplice.[7][8] With the appearance, he became the first-ever player from Mongolia to appear in the Czech top division.[9][10][11] On 16 November 2023, he made his Czech Cup debut in a 1–2 Fourth Round defeat to FK Jablonec.[12]