While she began work in features following her departure from "NYPD Blue", her subsequent television work was more successful than many of her film credits. A memorable recurring guest role as Faye, the strong-willed love interest of the radio psychiatrist, in the 1998-1999 season of NBC's "Frasier" kept her in the public eye, as did work in TV-movies, notably as the feminist painter in HBO's biopic "Mary Cassatt: American Impressionist" and as a daring field agent in ABC's "ATF" (both 1999). Later that year, Brenneman returned to regular series work, as creator, executive producer, and star of the CBS drama "Judging Amy". Based partially on the life of her own mother, Judge Frederica Brenneman, the series followed Judge Amy Gray (Brenneman), a recent divorcee who moves with her young daughter from New York City to her Hartford, Connecticut hometown, living in the family home with her mother and brother and pursuing a more satisfying job as a juvenile court judge. The show, likened to "Providence" in its theme and approach, (and also the coincidental physical similarities between Brenneman and "Providence" star Melina Kanakaredes), was an unexpected hit, and CBS quickly ordered a full season of episodes.

In 1995, Brenneman began the move into feature film work with supporting parts in "Casper", as Christina Ricci's mother, the romantic comedy "Bye Bye, Love", as Paul Reiser's ex-wife and "Heat", as Robert De Niro's love interest. She next teamed with William Petersen and Mark Wahlberg in the thriller "Fear" and starred opposite Sylvester Stallone in the disaster actioner "Daylight" (both 1996). Brenneman was co-producer of the independent feature "Nevada" (1997), which she additionally starred in as part of an ensemble cast of actresses including Kirstie Alley and Gabrielle Anwar. In 1998 she took on the morally ambiguous role of unhappily married and unfaithful Mary in the bleak "Your Friends and Neighbors", Neil LaBute's harsh look at sexual politics. Less memorable was her turn in Donal Lardner Ward's unremarkable directorial debut "The Suburbans" (1999), as the longtime girlfriend of a has-been rocker (Ward) whose titular band gets an unexpected second chance at stardom fifteen years after their lone hit. She was back among a host of strong actresses (e.g., Holly Hunter, Glenn Close, Calista Flockhart) in the Sundance screened "Things You Can Tell by Just Looking at Her" (aired on Showtime in 2001).

After a short hiatus from making films, Brenneman returned in “Off the Map” (2005), a well-reviewed drama about an eccentric family (Joan Allen, Sam Elliott and Valentina DeAngelis) living on the fringe of society in the New Mexico desert whose lives are altered by an IRS agent (Jim True-Frost) suffering from inner demons that eventually dissipate into sparse, idyllic land. Brenneman played the adult version of the family’s daughter, Bo, narrating the events that took place that one fateful summer in 1974. Brenneman was then part of the strong ensemble cast in Rodrigo Garcia’s feature drama, “Nine Lives” (2005), playing the ex-wife of a man (William Fichtner) who suddenly finds herself in love with him again after the death of his second wife.