She is known for her film roles such as Rachel Lapp in Witness (1985), for which she received Golden Globe and BAFTA nominations; Charlie in Top Gun (1986); Made in Heaven (1987); The House on Carroll Street (1988); and as Katheryn Murphy in The Accused (1988).

Her next high-profile role was that of flight instructor Charlotte Blackwood (call sign "Charlie") in the 1986 fighter-pilot film Top Gun starring Tom Cruise.

[13] McGillis played the part of caretaker for Miss Venable (Jessica Tandy) in 1988's The House on Carroll Street, which also starred Jeff Daniels.

She overhears a suspicious conversation in the house next door and suspects that she's stumbled on a conspiracy to smuggle Nazi war criminals into the United States.

[16] She played the suspect in the disappearance of a young woman in The Monkey's Mask, an international lesbian cult film from 2000 starring Susie Porter.

[22] Her stage work includes: Don Juan (1982), The Sea Gull (1985), Peccadillo (1985), The Merchant of Venice (1988), Twelfth Night (1989), Mary Stuart (1990), The Merry Wives of Windsor (1990), Hedda Gabler (1994), Mourning Becomes Electra (1997), A Midsummer Night's Dream (1999), Measure for Measure (1999) and The Graduate (2004), together with additional roles in Love for Love, Six Characters in Search of an Author, Three Sisters and The Winter's Tale.

[24] She had a role in the 2010 vampire film Stake Land,[25] directed by Jim Mickle,[26] starring alongside Nick Damici, Connor Paolo and Danielle Harris.

[28] She starred in Ti West's 2011 thriller The Innkeepers[29], We Are What We Are and Tio Papi in 2013, Grand Street, Love Finds You in Sugarcreek, Ohio (which was McGillis's third Amish-themed film), Z Nation, and an episode of Sisters of Mercy in 2014, and Blue in 2015.

An Uncommon Grace on Hallmark Channel was McGillis's fourth Amish themed film[30] and she had the lead role in Mother of All Secrets in 2017 as Rose Lewis.

The Centurion, a 110-foot schooner valued at $1.5 million owned by McGillis and her then-husband, Fred Tillman, was destroyed by fire in April 1996 at a marina in Dania, Florida.

They had met in 2000 when Leis was a bartender at the Caribbean Bar Grill & Brewery[41] in Key West, Florida,[42] which McGillis owned with her then-husband.