Nystrom established a hard-working style similar to his father's, which helped earn him an invite to play with the US National Development Program (USDP). He played 55 games for USDP in the North American Hockey League in 1999–2000, scoring seven goals and 23 points. He split the 2000–01 season with the national under-18 program and the junior team in the United States Hockey League, also representing the United States at the 2001 IIHF World U18 Championships. He later represented the United States at the 2002 and 2003 World Junior Ice Hockey Championships.