In 1990, while dealing blackjack at a charity event, Jeri met investment banker and future political candidate Jack Ryan. The couple married on June 15, 1991 and had a son, Alex, on August 15, 1994. Throughout the marriage, Ryan and her husband took turns commuting between Los Angeles and Chicago for their careers, but finally divorced on August 27, 1999. Although Ryan mentioned in an interview for Star Trek that the frequent separations had been difficult for the marriage; the reasons for the divorce were kept sealed at their mutual request. Five years later, when Jack Ryan's Senate campaign began, the Chicago Tribune newspaper and WLS-TV, the local ABC affiliate, sought to have the records released. Both Jeri and Jack agreed to make their divorce records public, but not the custody records, claiming that their release could be harmful to their son.

On June 22, 2004, Los Angeles Superior Court Judge Robert Schnider agreed to release the custody files. The decision generated much controversy because it went against both parents' direct request and because it generally reversed the early decision to seal the papers in the best interest of the child. It was revealed that six years previously, Jeri had accused Jack Ryan of asking her to perform sexual acts with him in public, and in sex clubs in New York, New Orleans, and Paris. Jeri Ryan described one as "a bizarre club with cages, whips and other apparatus hanging from the ceiling." Jack Ryan denied these allegations. Although Jeri Ryan refused to comment on the matter during the campaign, the document disclosure led Jack Ryan to withdraw his Republican candidacy for an open United States Senate seat in Illinois. He was replaced as the Republican candidate for his Senate seat by Alan Keyes who was easily defeated by the Democratic candidate, Barack Obama.

Ryan's avocation, according to statements she has made in interviews, is gourmet cooking. While starring in Boston Public she moonlighted on weekends in the kitchen of the Los Angeles restaurant The House. In 2003, Ryan met French chef Christophe Émé at a chef's charity event. The two would eventually begin a relationship, and Émé moved in with Ryan and her son Alex in their San Fernando Valley home. In February 2005, Ryan, a "lifelong Francophile", opened—in partnership with Émé—the restaurant Ortolan. Located on Third Street in Los Angeles, California, the restaurant serves French food with a modern interpretation. And they have appeared on Iron Chef America, where Émé and one sous-chef challenged Iron Chef Masaharu Morimoto and his two sous-chefs. Ryan married Émé in the Loire Valley, France, on June 16, 2007. On September 7, 2007, Ryan announced that she and Émé were expecting their first child together, a daughter, in March 2008. On March 2, 2008, Ryan gave birth to daughter Gisele Émé in Los Angeles, California.

• "Shark" .... Jessica Devlin (38 episodes, 2006-2008)
       - Wayne's World 3: Killer Shark (2008) TV episode (credit only) .... Jessica Devlin
       - One Hit Wonder (2008) TV episode (credit only) .... Jessica Devlin
       - Leaving Las Vegas (2008) TV episode (credit only) .... Jessica Devlin
       - Bar Fight (2008) TV episode (credit only) .... Jessica Devlin
       - Partners in Crime (2008) TV episode .... Jessica Devlin
        (33 more)
• "Boston Legal" .... Courtney Reese (2 episodes, 2006)
       - BL: Los Angeles (2006) TV episode .... Courtney Reese
       - Spring Fever (2006) TV episode .... Courtney Reese
• "The O.C." .... Charlotte Morgan (7 episodes, 2005)
       - The Anger Management (2005) TV episode .... Charlotte Morgan
       - The Swells (2005) TV episode .... Charlotte Morgan
       - The Perfect Storm (2005) TV episode .... Charlotte Morgan
       - The Last Waltz (2005) TV episode .... Charlotte Morgan
       - The End of Innocence (2005) TV episode .... Charlotte Morgan
        (2 more)
• "Two and a Half Men" .... Sherri (2 episodes, 2004-2005)
       - A Low, Guttural Tongue-Flapping Noise (2005) TV episode .... Sherri
       - Bad News from the Clinic (2004) TV episode .... Sherri
• The Commuters (2005) (TV) .... Anne
• "Boston Public" .... Ronnie Cooke (59 episodes, 2001-2004)
       - Chapter Eighty-One (2004) TV episode .... Ronnie Cooke
       - Chapter Eighty (2004) TV episode .... Ronnie Cooke
       - Chapter Seventy-Nine (2004) TV episode .... Ronnie Cooke
       - Chapter Seventy-Eight (2004) TV episode .... Ronnie Cooke
       - Chapter Seventy-Seven (2004) TV episode .... Ronnie Cooke
        (54 more)
• Sudbury (2004) (TV) .... Gillian Owens
• Down with Love (2003) .... Gwendolyn
  ... aka Down with Love - Zum Teufel mit der Liebe! (Germany)
• "Star Trek: Voyager" .... Seven of Nine / ... (102 episodes, 1997-2001)
  ... aka Voyager (USA: short title)
       - Endgame (2001) TV episode .... Seven of Nine
       - Renaissance Man (2001) TV episode .... Seven of Nine
       - Homestead (2001) TV episode .... Seven of Nine
       - Natural Law (2001) TV episode .... Seven of Nine
       - Friendship One (2001) TV episode .... Seven of Nine
        (97 more)
• Dracula 2000 (2000) .... Valerie Sharpe