The fifth season of the American fictional drama television series ER first aired on September 24, 1998, and concluded on May 20, 1999. The fifth season consists of 22 episodes, including the series' 100th episode.

Medical student Lucy Knight (Kellie Martin) begins her studies in the ER. As she spends time learning the layout and staff of the ER, we learn of Dr. Anna Del Amico's departure. Carter is reminded of himself as he watches Knight learn and practice. The two have a large number of conflicts before they find a way to work together. Elizabeth Corday begins her surgical internship all over again in order to keep her job at the hospital, and ends her relationship with fellow surgeon Peter Benton. Benton finds out that his son is hearing impaired, and he considers a cochlear implant. Eventually, he decides against it. Kerry Weaver applies for a full-time chief of emergency medicine post, but the post goes to an East Coast doctor, Amanda Lee. Dr. Lee soon develops a more-than-professional interest in Mark Greene with Lee being revealed to be a fraudulent psychopath who later leaves under cloudy circumstances.

Greene does a paramedic ride-along, and Doug Ross has at last settled down with Carol Hathaway. While on probation after performing a risky procedure during the fourth season, Ross breaks protocol again by informing a mother how to alter the medication given to her disabled son. She uses this information to kill her son, leaving Ross under fire. He resigns and moves to Seattle.

Original executive producers John Wells and Michael Crichton reprised their roles. Lydia Woodward, Carol Flint, and Christopher Chulack all returned as executive producers. Flint left the crew with the close of the fifth season. Co-executive producer Walon Green returned for the fifth season but left the series mid-season. Fourth season producer Neal Baer and fourth season co-producer Jack Orman were promoted to supervising producers for the fifth season. Fourth season producer Penny Adams and co-producers Wendy Spence Rosato, Richard Thorpe, and Michael Salamunovich all returned to their roles. Spence Rosato was promoted to producer mid-season. Fourth season executive story editor Samantha Howard Corbin was promoted to co-producer for the fifth season but left the crew mid-season. She was replaced as co-producer by regular director Jonathan Kaplan.

Producers Wells, Woodward, Flint, Baer, Orman, Corbin, and Greene continued to write episodes. Wells wrote two episodes, Woodward wrote four episodes, and Flint wrote five episodes. Baer wrote two episodes, Orman wrote three episodes, and Corbin and Greene each contributed to one episode before their departure. Regular writer and previous technical advisor Joe Sachs was promoted to story editor for the fifth season and contributed to two episodes. Former producers David Mills and Paul Manning continued to write for the series, Mills contributed to two further episodes, and Manning scripted one more episode. Fourth season writer Linda Gase returned and contributed to two more episodes. New writer Christopher Mack wrote a single episode.

Producers Chulack and Kaplan served as the seasons regular directors. Chulack helmed five episodes and Kaplan directed four. Cinematographer and co-producer Thorpe directed a further episode. Regular directors Lesli Linka Glatter, Félix Enríquez Alcalá, and Rod Holcomb all returned to direct further episodes. Other returning directors include executive producer John Wells, Christopher Misiano, David Nutter, and T.R. Babu Subramaniam. Cast member Laura Innes made her series directing debut with a fifth-season episode. Other new directors were Steve De Jarnatt and Dave Chameides, each with a single episode.