Jonathan Frakes was born on August 19, 1952 in Bellefonte, Pennsylvania to parents Doris and James Frakes. Jonathan, younger brother Daniel, and his parents moved to Bethlehem, Pennsylvania several years later where his father became a professor of English at Lehigh University. Frakes attended the Bethlehem School District and graduated from Liberty High in 1970. Frakes continued his education at Pennsylvania State University, where he began to pursue a career by majoring in Psychology. However, Frakes realized that his passion lay elsewhere, and promptly changed his major to Theatre Arts. He graduated in 1974, and pursued a Master's Degree at Harvard. Frakes became a member of Harvard's acting company, the Loeb Drama Center, and graduated in 1976.

Post graduation, Frakes moved to New York City to pursue a career in acting. He joined "The Impossible Ragtime Theatre," the theatre that Brian Dennehy also credits for jumpstarting his own career, and was part of several off-Broadway productions. Frakes moved to Los Angeles in the late 1970s with hopes that the west coast would provide opportunities for him to begin work on both the small and silver screens. The move proved very successful for Frakes, as he landed a recurring role as Tom Carroll on the soap opera The Doctors. Frakes continued to have roles in numerous popular television shows throughout the 1970s and early 1980s, such as Charlie's Angels, Fantasy Island, Dukes of Hazzard, Bare Essence, and numerous others, including a recurring role on The Waltons.

In 1985 and 1986, the role of Stanley Hazard in the miniseries North and South and North and South: Book II proved to be monumental for Frakes. First, the two series were overwhelming successes, and Frakes garnered critical acclaim for his performance. Also, it was on the set of North and South that Frakes met soap opera star Genie Francis, who played Brett Main Hazard. Frakes reportedly fell in love with Francis on the set, and they were married two years later on May 28, 1988.

The role which would end up exemplifying and marking Frakes' career was offered to him in 1987. Frakes auditioned for and landed the role of Commander William T. Riker on the new show Star Trek: The Next Generation, a continuation of the 1960s series Star Trek, that takes place 95 years after that of the original series. Frakes was praised for his strong and convincing portrayal of the character, whose job it was to provide for an efficiently run ship and crew with a military-like bearing. Interestingly, it was on the set of The Next Generation that Frakes showcased his musical talents by forming the musical band The Sunspots with fellow cast members Michael Dorn, Patrick Stewart, and Levar Burton. The Sunspots appeared on Brent Spiner's 1991 album "Ol' Yellow Eyes is Back," and Frakes trombone skills were even showcased on the 1994 Phish album Hoist. Frakes continued the role of Riker on the series into the mid 1990s, but during the series, he began to invest his time in other endeavors.

While working on Star Trek: The Next Generation, Frakes became interested in the production side of television and film. He spent an immense amount of time in the editing room, and worked closely with directors, editors, and producer Rick Berman. Berman allowed Frakes to make his directing debut with the Star Trek: The Next Generation episode "The Offspring" and the production staff was remarkably impressed. Due to the success of the show, the film Star Trek: Generations was filmed in which Frakes again portrayed Commander Riker. After receiving lukewarm reviews, Frakes expanded upon his directing career by directing several other episodes of the series, and made his directorial film debut with Star Trek: First Contact. The movie was a colossal success with "Trekkies," "Non-Trekkies," and critics alike. First Contact was labeled the best sci-fi film of the year, and is credited as the best and highest-grossing Star Trek film to date. According to Rob Blackwelder of splicedwire.com, "For non-Trekkers, this is a great, free-standing special-effects adventure with much more fleshy characters than your average sci-fi yarn. But, there are also plenty of nods to Star Trek aficionados." On the set, Frakes set the bar with an efficient, no-time-wasted directing style that earned him the nickname "Two-Takes Frakes."

Throughout the late 1990s, Frakes pursued several other endeavors that brought him success. From 1995 through 1998, Frakes provided the voice for Dr. Xanatos on the popular animated series Gargoyles. In 1999, Frakes directed the next Star Trek film, Star Trek: Insurrection, which included the same Next Generation cast as the previous two films. It was a large success with fans as well as monetarily despite mixed critical reviews. Taking place on a planet of eternal life, the film was acclaimed for its relatable themes, energetic battle scenes, fast pace, and good humor. Frakes was also a cast member on Star Trek: Deep Space Nine, Star Trek: Voyager, and Star Trek Enterprise, all debuting throughout the mid to late 1990s, making him the only cast member besides Majel Barrett to appear in every Trek series other than the original. Also in the late 1990s, Frakes became a father to two children. Son Jameson was born in 1997 and daughter Elizabeth was born in 1997.

Frakes began his career as a producer in 1999 with the successful, award-winning television show Roswell which he also directed. He directed the film Clockstoppers starring French Stewart and Julia Sweeney in 2002, and though it was not a resounding success, the adventurous and fun film was enjoyed by audiences. In 2004, Frakes directed the family-fun movie Thunderbirds, an adaptation of the original 1960s British TV series created by Gerry Anderson. Thunderbirds proved to be a film full of relatable young heroes perfect for children, and an appropriate homage for fans of the original series.

Currently, Frakes owns Goepp Circle Productions, which works in coordination with Paramount Pictures. In 2006, Frakes directed the made for TV movie The Librarian II: Return to King Solomon's Mines starring Noah Wyle. Frakes resides in Los Angeles with his wife Genie, where he continues to act and direct.