Within weeks of J. Howard Marshall's death, Smith and her husband's son, E. Pierce Marshall, battled over her claim for half of her late husband's US$1.6 billion estate. She temporarily joined forces with J. Howard's other son, James Howard Marshall III, whom the elder Howard had disowned. Howard III claimed J. Howard orally promised him a portion of his estate; like Smith, Howard III was also left out of J. Howard's will. The case has gone on for more than a decade, producing a highly publicized court battle in Texas and several judicial decisions that have gone both for and against Smith in that time.

In 1996, Smith filed for bankruptcy in California as a result of a $850,000 judgment against her for sexual harassment of an employee. As any money potentially due to her from the Marshall estate was part of her potential assets, the bankruptcy court involved itself in the matter.

Smith claimed J. Howard orally promised her half of his estate if she married him. In September 2000, a Los Angeles bankruptcy judge awarded her $449,754,134. In July 2001, Houston judge Mike Wood affirmed the jury findings in the probate case by ruling that Smith was entitled to nothing and ordered Smith to pay over $1 million in fees and expenses to Pierce's legal team. The conflict between the Texas probate court and California bankruptcy court judgments forced the matter into federal court.

In March 2002, a federal judge vacated the California bankruptcy court's ruling and issued a new ruling but reduced the award to $88 million. In December 2004, a three-judge panel of the U.S. 9th Circuit Court of Appeals reversed the March 2002 decision, on the reasoning that the federal courts lacked jurisdiction to overrule this probate decision.

The U.S. Supreme Court decided in September 2005 to hear the appeal of that decision. The Bush administration subsequently directed the Solicitor General to intercede on Smith's behalf out of an interest to expand federal court jurisdiction over state probate disputes. After months of waiting, Smith and her stepson Pierce learned of the Supreme Court's decision on May 1, 2006. The justices unanimously decided in favor of Smith; Justice Ruth Bader Ginsburg wrote the majority opinion. The decision did not give Smith a portion of her husband's estate, but affirmed her right to pursue a share of it in federal court. On June 20, 2006, E. Pierce Marshall died at age 67 from an "aggressive infection". His widow, Elaine T. Marshall, now represents his estate. The case was remanded to the 9th Circuit to adjudicate the remaining appellate issues not previously resolved.

After Anna’s death, the New York Times reported that the case over the Marshall fortune "is likely to continue in the name of Ms. Smith’s infant daughter." The current situation is that Anna Nicole Smith's estate will not inherit any of her late husband's estate. Following the decision by the Appeals Court for the Ninth Circuit, lawyers for the estate of Anna Nicole Smith requested the appeal be heard before the entire 9th circuit. However on May 6, 2010 the appeal was denied, leaving an appeal to the United States Supreme Court as the final legal avenue for the long running dispute which dates back almost 15 years

Although her film appearances in The Hudsucker Proxy and Naked Gun 33⅓: The Final Insult were highly publicized in 1994, little was done to further Smith's acting career. Her first major role was as Colette Dubois, a retired spy seeking revenge for the murder of her husband, in the action/thriller To the Limit (1995).

Smith next starred in the action/thriller Skyscraper (1997), which she also produced, as a helicopter pilot, Carrie Wisk, who lands on a high rise building and, upon learning it has been taken over by terrorists, becomes engaged in a deadly fight to save hostages.

Both films, and Smith's performances in them, were critically panned. During the course of the litigation over her late husband's estate, her career stalled. Her legal battle, her increasing weight, and her reportedly bizarre behavior made her regular fodder for late night television comedians.