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Kilgore, the first American-born woman to earn U.S. Soccer's top-level Pro License, was an assistant under Andonovski for 1 1/2 years and will lead the team while a search for a permanent coach is conducted.
SEE RELATED STORY: USA coach Vlatko Andonovski resigns after World Cup exit: ESPN sources
Andonovski's resignation comes less than two weeks after the United States was knocked out of the Women's World Cup earlier than ever before.
"While we are all disappointed by the outcome at this year's World Cup, I am immensely proud of the progress this team has made, the support they've shown for each other, and the inspiration they've provided for players around the world. I will be forever thankful to the U.S. Soccer Federation for giving me the chance to coach this remarkable team," Andonovski said in a statement.
Previously, Kilgore was an assistant coach with the Houston Dash in the National Women's Soccer League and worked with numerous U.S. youth women's national teams. She's spent 15 years in the college game, as a head coach at UC-Davis and an assistant at Pepperdine before landing the top job there.
Kilgore will lead the U.S. team in a pair of exhibition matches against South Africa on Sept. 21 in Cincinnati and on Sept. 24 in Chicago.
The four-time tournament champions struggled throughout the World Cup. A victory over Vietnam to kick off the group stage was followed by a pair of draws against the Netherlands and Portugal - barely enough to get the team into the knockout stage.
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The Americans played well in the Round of 16 against Sweden, but ultimately fell on penalties after a scoreless tie. The U.S. scored just four goals over the course of the tournament. The United States had never finished worse than third at the World Cup.
U.S. Soccer Sporting Director Matt Crocker, appointed to the job in April, will lead the search for a new coach. Crocker has launched an in-depth analysis of the women's program aimed at ensuring the team remains competitive.
"It's imperative that we continue to evolve and innovate, and we are excited about the path that lies ahead," Crocker said in a statement. "We understand the challenges and have engaged with stakeholders from various corners of our sport - players, coaches, and other individuals within the soccer landscape. The insights and perspectives gathered during these discussions have been instrumental in shaping our forward-looking plan."
The 46-year-old Andonovski was named coach of the United States in October 2019, taking over for Jill Ellis, who led the United States to back-to-back World Cup titles. He finished 51-5-9 during his time with the team and was 3-2-5 in major tournaments.
"We want to extend our deepest gratitude to Vlatko for his dedication to the Women's National Team," U.S. Soccer president Cindy Parlow Cone said in a press release. "We know he will continue to contribute to the growth of the women's game in the United States and wish him well in his future endeavors."
The United States also finished with a disappointing bronze medal at the Tokyo Olympics. Afterward, Andonovski turned his attention on developing young players ahead of the World Cup. Some of the players who emerged were Sophia Smith, last year's U.S. Soccer Player of the Year, and Trinity Rodman.
Fourteen players on the U.S. roster were appearing in their first World Cup, and 12 had never played in a major tournament.
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The United States was also bitten by injuries in the run-up to the tournament, losing a pair of key players. Mallory Swanson injured her knee during a friendly in April, and captain Becky Sauerbrunn couldn't recover from a foot injury in time.
Promising young forward Catarina Macario tore her ACL playing for her club team Lyon last year and also wasn't ready to play in the World Cup.
Andonovski's predecessor on the U.S. team, Ellis, was named coach of the team in 2014 and led the U.S. to eight overall tournament titles, including victories at the World Cup in 2015 and 2019. Over the course of her tenure, the United States lost just seven matches.
Ellis was asked about the job Thursday while at the World Cup in Sydney. She heads the FIFA Technical Study Group.
"What I would hope in this (hiring) process (is) that it's robust, it's diverse. It has to be," Ellis said. "This is a critical hire. And I think it has to be the right person."
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AP Sports Writer John Pye contributed to this report.