In 1979, Cornwell began working as a reporter for The Charlotte Observer, initially editing TV listings, then moving to features, and finally becoming a reporter covering crime. In 1980, she received the North Carolina Press Association's Investigative Reporting Award for a series on prostitution. She continued at the newspaper until 1981, when she moved to Richmond, Virginia with her first husband, Charles Cornwell (married in 1980), who enrolled at the Union Theological Seminary. The same year she began working on the biography of Ruth Bell Graham, A Time for Remembering: The Ruth Bell Graham Story (renamed Ruth, A Portrait: The Story of Ruth Bell Graham in subsequent editions), which was published in 1983. The biography gained a Gold Medallion Book Award from the Evangelic Christian Publishers Association in 1985. It also, however, was a major blow to her friendship with Graham – they weren't on speaking terms for 8 years following the book's publication.

Cornwell began work on her first novel in 1984, about a male detective named Joe Constable and met Dr. Marcella Farinelli Fierro, a medical examiner in Richmond, and subsequent inspiration for the character of Dr. Kay Scarpetta. In 1985, she took a job at the Office of the Chief Medical Examiner of Virginia. She worked there for six years, first as a technical writer and then as a computer analyst. She also volunteered to work with the Richmond Police Department. Cornwell wrote three novels that she says were rejected before the publication in 1990, of the first installment of her Scarpetta series, Postmortem, based on real-life stranglings in Richmond in the summer of 1987. The novel won her various awards including the British John Creasey Award, the French Prix du Roman d'Adventure and the American Edgar Award.

The Scarpetta novels include a great deal of detail on forensic science. The initial resolution to the mystery is found in the forensic investigation of the murder victim's corpse, although Scarpetta does considerably more field investigation and confrontation with suspects than real-life medical examiners. The novels generally climax with action scenes in which Scarpetta and her associates confront, or are confronted by, the killer or killers, usually concluding with the death of the killer. The novels are considered to have influenced the development of popular TV series on forensics, both fictional, such as CSI: Crime Scene Investigation, and documentaries, such as Cold Case Files.

Other significant themes in the Scarpetta novels include health, individual safety and security, food, family, and the emerging sexual self-discovery of Scarpetta's niece. Often, conflicts and secret manipulations by Scarpetta's colleagues and staff are involved in the story-line and make the murder cases more complex. Although scenes from the novels take place in a variety of locations around the United States and (less commonly) internationally, they center around the city of Richmond, Virginia.

There are two remarkable style shifts in the Scarpetta novels. Starting from The Last Precinct (2000), the style changes from past tense to present tense. Starting from Blow Fly (2003), the style changes from a first person to a third person, omniscient, narrator. Events are even narrated from the viewpoint of the murderers. Before Blow Fly the events are seen through Scarpetta's eyes only, and other points of view only appear in letters that Scarpetta reads.

Cornwell shifted back to a first-person perspective in the Scarpetta novel Port Mortuary (2010).

In addition to the Scarpetta novels, Cornwell has written three pseudo-police fictions, known as the Trooper Andy Brazil/Superintendent Judy Hammer series, which are set in North Carolina, Virginia, and off the mid-Atlantic coast. Besides the older-woman/younger-man premise, the books include discomforting themes of scatology and sepsis.

Jack the Ripper

Cornwell has been involved in a continuing, self-financed search for evidence to support her theory that painter Walter Sickert was Jack the Ripper. She wrote Portrait of a Killer: Jack the Ripper—Case Closed, which was published in 2002 to much controversy, especially within the British art world and among Ripperologists. Cornwell denied being obsessed with Jack the Ripper in full-page ads in two British newspapers and has said the case was "far from closed". In 2001, Cornwell was criticized for allegedly destroying one of Sickert's paintings in pursuit of the Ripper's identity. She believed the well-known painter to be responsible for the string of murders and had purchased over thirty of his paintings and argued that they closely resembled the Ripper crime scenes. Cornwell also claimed a breakthrough: a letter written by someone purporting to be the killer, had the same watermark as some of Sickert's writing paper. Ripper experts noted, however, that there were hundreds of letters from different authors falsely claiming to be the killer, and the watermark in question was on a brand of stationery that was widely available.

In 2004, Cornwell assigned management of her financial matters to New York-based Anchin, Block & Anchin, managed by principal Evan Snapper. Agreeing to pay the firm a base rate of $40,000/month, her lawyer later claimed that Cornwell had hired Snapper to insulate herself from her money due to her ongoing mental health issues, and that Snapper knew this and took advantage of her over her four-and-a-half-year relationship with the company.

Cornwell fired the firm after discovering in July 2009 that the net worth of her and her company, Cornwell Entertainment Inc., despite having above $10 million in earnings per year during the previous four years, was a little under $13 million, the equivalent of only one year's net income. After Cornwell filed the lawsuit, Snapper pleaded guilty to violating campaign finance regulations. The court case opened in January 2013, with Cornwell suing the firm for a combined sum of $100M. On February 19, a Boston jury awarded Cornwell US$50.9 million (£33.4 million).