Jankto came out in February, saying he wanted to live his life "in freedom". His announcement was met with support from Brazil's Neymar, the English Premier League, LaLiga and European soccer's governing body UEFA.
The midfielder has played 16 games in all competitions for Sparta this term, having joined on loan from Spanish side Getafe.
"In recent years, and especially the last year, so many things have accumulated around me that it is better to slow down and think about my health as well," he said in an Instagram post.
"It wasn't the best sporting year for me ... I am all the more saddened that my health and mental state will not allow me to continue my pursuit of the title and cup."
Sparta said in a statement that Jankto would step aside from first team duties due to "personal matters" and that the club had met with him following a traffic incident on Tuesday.
Sparta lead the Czech top flight with 61 points after 27 games, two points above second-placed Slavia Prague. The two Prague teams are due to meet in the Czech Cup final in May.
