Feilhaber was six years old when his family moved from Brazil to settle in the United States and attended Nottingham Country Elementary in Katy, Texas. He spent approximately eight years in the New York City suburb of Scarsdale where he played for the local soccer team, the Scarsdale Lightning. In 1996, he led the team and won the New York State Cup for the U-12 division. He attended Northwood High School in Irvine, California where he was a standout midfielder on the school’s soccer team. He also played club soccer for the Irvine Strikers, winning various youth national titles. He was coached by youth coach Don Ebert.

After graduating in 2003 he played college soccer at the University of California, Los Angeles (UCLA), where he became a mainstay in the Bruins’ midfield. At UCLA he was roommates with future national teammate Jonathan Bornstein. Feilhaber made the team as a walk-on, rather than being recruited with a scholarship offer. After his second year at UCLA Feilhaber was called up by the U.S. U-20 national soccer team to play in the 2005 FIFA World Youth Championship in the Netherlands.

His performances in the tournament caught the attention of scouts from several European teams and, after representing the U.S. in the 2005 Maccabiah Games in Israel where he won a silver medal playing for it alongside Jonathan Bornstein and Leonid Krupnik, Feilhaber signed for Hamburger SV in July 2005. In the 2005–06 season, Feilhaber played with the Hamburg reserve team in the third division, or Regionalliga.

Feilhaber was called up twice to the full U.S. national team for friendlies against Scotland on November 12, 2005, and Germany on March 22, 2006, but did not play in either game.

On October 12, 2006, Feilhaber made his Bundesliga debut, coming on as a second-half substitute in a 2–1 home loss to Schalke 04. His first start came on October 22, 2006, when he played ninety minutes in a 2–1 win against Bayer Leverkusen, Hamburg’s first win of the season.

On November 30, 2006, he turned down an offer from Andreas Herzog to play for Austria and said that he would instead focus on earning a place on the U.S. national team.

On August 9, 2007, Feilhaber obtained a work permit to play for newly promoted Premier League side Derby County. His signing was completed on August 10, 2007, and Feilhaber made his debut for the club on September 17, 2007, coming on as an eightieth-minute substitute in a 1–0 win over Newcastle United.

On March 15, 2007, Feilhaber was again placed on the 24-man roster by coach Bob Bradley for friendly matches against Ecuador and Guatemala. Feilhaber made his first career start for the U.S. team in the March 25, 2007, game against Ecuador, and scored his first international goal against China on June 2, 2007. He scored the game-winning goal on a volley in the 2007 Gold Cup final on June 24, 2007, against Mexico.

On August 15, 2008, Feilhaber signed with Danish Superliga team Aarhus Gymnastikforening, commonly known as AGF. He made his debut for the club on September 1, 2008, coming on as a 59th-minute substitute in a 0–3 loss to FC Nordsjælland. He scored his first Superliga goal and was named Man of the Match against Randers on July 27, 2009.

Feilhaber made his debut for AGF in August 2008 and managed to play 58 games and scoring eight goals. His performance in the white jersey paved the way for his participation in the World Cup finals in South Africa with the U.S. national team.

After more than a year since his last action with the senior team, Feilhaber was named to the U.S. roster for the 2009 FIFA Confederations Cup. Along with former UCLA teammate Jonathan Bornstein and fellow UCLA alum Carlos Bocanegra, Feilhaber played in the upset of top-ranked Spain in a semi-final game on June 24, 2009. He orchestrated the second goal, rounding Gerard Pique to find Landon Donovan, who found Clint Dempsey for the finish in the center. He then appeared in the final, in which the U.S. fell to the country of his birth, Brazil 3–2.

After the winter break, AGF continued their winning streak in order to secure promotion to the Danish Superliga, but Feilhaber was mostly benched with a minor injury. On April 16, 2011, on the last day of the American transfer window, AGF sold Feilhaber to MLS.

Following the 2012 season, New England did not exercise his option. He was later traded to Sporting Kansas City in exchange for a 2014 MLS SuperDraft first-round pick, a 2015 MLS SuperDraft second-round pick, and allocation money. Benny quickly found success in Kansas City, featuring as a starter for the side that captured the 2013 MLS Cup.

He married his wife, Michele, on December 15, 2012. Feilhaber has a daughter named Sofia and a daughter named Julia.

The 2015 season saw a return to top form for Feilhaber. He became a focal point in the entire scheme of attack, being more of a playmaker than ever before. As of September 18, 2015, he had amassed in 31 competitive appearances, 12 goals and 19 assists. In November 2015, he was named one of the three finalists for both the 2015 MLS Landon Donovan MVP Award.

Feilhaber was traded to expansion side Los Angeles FC on January 3, 2018, in exchange for $400,000 in allocation money. In 34 appearances for the franchise in its inaugural season he would score 3 goals and notch 6 assists. Despite playing all but one competitive match for the club that year, Feilhaber found himself out of contract at the end of the season and became a free agent.

On January 11, 2019, Feilhaber joined Colorado Rapids.

On May 8, 2019, Feilhaber was traded to Sporting Kansas City. He debuted on May 18 in a 1–1 draw with the Vancouver Whitecaps FC.

After leaving Kansas City at the end of their 2019 season, Feilhaber officially announced his retirement from playing professional soccer on March 11, 2020.