Ema Kapustová made her international debut at the 2019 Youth World Championships in Osrblie, achieving a 21st place as her best result. She later participated in the Youth Olympic Games in Lausanne in January 2020, finishing eighth in the sprint event.[3] Later Kapustová made her IBU Junior Cup debut and achieved a top-ten finish placement. In January 2021, she debuted in the IBU Cup but initially struggled despite good shooting results. However, she won a bronze medal at the Youth World Championships in Obertilliach and improved from 30th to 9th place in the pursuit event.[4] In the 2021/22 season, she primarily competed in junior events, with a highlight being a top-10 finish at the Junior World Championships. She earned her first IBU Cup points in the following season, including a victory in the Junior Cup in a single-mixed relay.
In the summer of 2023, Kapustová won silver medals in the sprint and pursuit events at the Summer Biathlon Junior World Championships in Osrblie. She made her World Cup debut in Östersund in the winter of 2023/24 and achieved her first pursuit competition after finishing 56th in the sprint in Hochfilzen. She notably improved her performance in Lenzerheide, finishing 41st in the sprint and 28th in the pursuit, earning her first World Cup points. Kapustová won her first medal in the senior category at the European Championships in Slovakia on January 24, 2024, finishing with the third-best time in the individual race.