Born to second-generation Italian American parents Frank Ruffalo (a construction painter) and Maria (a hairdresser), he spent his teen years in Virginia Beach, Virginia where he graduated from First Colonial High School. He then moved with his family to San Diego, California and later to Los Angeles, California where he took classes at the Stella Adler Conservatory and co-founded the Orpheus Theatre Company. With the OTC, he wrote, directed, and starred in a number of plays, but overall his luck with acting was not great, and he spent the next 9 years earning his living being a bartender. He had minor roles in films like The Dentist (1996), the low-key crime comedy Safe Men (1998) and Ang Lee's acclaimed Civil War Western Ride With the Devil (1999).

Through a chance meeting with writer Kenneth Lonergan, Ruffalo began collaborating with Lonergan and appeared in several of his plays, including the original cast of This Is Our Youth (1998), which led to Ruffalo's role as Laura Linney's troubled, aimless drifter brother Terry in Longeran's acclaimed, Academy Award-nominated 2000 film You Can Count on Me. He received strongly favorable reviews for his performance in this film, often earning comparisons to the young Marlon Brando, and won awards from the Los Angeles Film Critics Association and Montreal World Film Festival.

This led to other significant opportunities, including the films XX/XY (2002), My Life Without Me (2003), Eternal Sunshine of the Spotless Mind (2004), and We Don't Live Here Anymore (2004), which is based upon two short stories written by Andre Dubus. He attracted controversy for his steamy sex scenes with Meg Ryan as a sleazy, potentially dangerous homicide cop in Jane Campion's dark psychosexual thriller In the Cut (2003), and appeared opposite Tom Cruise as another homicide detective in Michael Mann's acclaimed crime-thriller Collateral (2004). More recently, to the disappointment of some fans of his dramatic acting skills, Ruffalo has cornered the market in romantic leads in so-called "chick flicks" like View From the Top (2002), 13 Going on 30 (2004), Just Like Heaven (2005) and Rumor Has It (2005).

In 2002, Ruffalo was diagnosed with a brain tumor and had surgery, which resulted in a period of partial facial paralysis, even though the tumor was found to be benign. He fully recovered from the paralysis and returned to good health as well as an active life and movie career.

He has been married to actress Sunrise Coigney since June of 2000, and they have two children: a son Keen born in 2001, and a daughter Bella born in 2005.

He is currently (June 2006) starring in Clifford Odets's 'Awake and Sing' at the Belasco Theater in New York, for which he won the Tony Award for Best Featured Actor in a Play.