The long established United Soccer League (USL) and the new breakaway North American Soccer League (NASL) will hold a one-off joint championship run by the federation in 2010.
The deal was reached after U.S Soccer refused to authorise either of the leagues, leaving North America without an official second tier.
Major League Soccer (MLS) is the first division in the United States and Canada but with no promotion or relegation in the region, USL has been run as a separate entity.
"We are extremely pleased that we were able to come to a solution that ensures we will have Division 2 professional soccer in the United States in 2010," U.S. Soccer president Sunil Gulati said in a statement.
"This agreement allows us to continue to develop the professional game in many important markets around the country, while at the same time working towards the long-term stability of Division 2 professional soccer."
The league will consist of two six-team conferences - the USL Conference and the NASL Conference.
The USL Conference will include teams from Austin, Minnesota, Portland, Puerto Rico, Rochester and Tampa Bay. The NASL Conference will consist of teams from Baltimore, Carolina, Miami, Montreal, St. Louis and Vancouver.
The schedule, television rights and details of the league format and rules have yet to be announced.
All pending claims between the USL and NASL will be dropped as part of the settlement, U.S Soccer said.
