His later credits include Riding in Cars with Boys, The Hole (both 2001), Ghost Ship, We Were Soldiers (both 2002), Love Object, Wrong Turn (both 2003), The Dark Knight Rises (2012), and The Neon Demon (2016).

On television, Harrington played "Joey" Quinn on Showtime's Dexter (2008–2013), Jack Bass on the CW's Gossip Girl (2009–2012), Alan Shepard in the ABC miniseries The Astronaut Wives Club (2015), Michael Rowan on CBS's Elementary (2018), and Louis Freeh on the second season of Spectrum's Manhunt (2020).

Dragnet (2003–2004), Harrington starred on the short-lived ABC sitcom Sons & Daughters (2006), which drew attention for its use of improvisation and absence of a traditional laugh track.

In his review of the episode for Entertainment Weekly, Ken Tucker commented, "In a very nice performance utterly unlike anything he does on Dexter, Harrington let his hair get all bed-heady and spoke in a mumble-mouth drawl as he set up his favorite sadistic game: He lays a gun on a table, and has someone count down from 10.

[14] On the sixth season of Elementary (2018), a contemporary spin on Sherlock Holmes, Harrington played Michael Rowan, a serial killer struggling with sobriety.