Balagueró began his filmmaking career with the short video projects El niño bubónico (1991) and La invención de la leche (1993). In 1994, Balagueró graduated to shooting on 35mm with the short film Alicia (1994). The film won the prize for Best Short film at the Sitges Film Festival. Balagueró returned with the short Days without Light (1995), which achieved similar success on the festival circuit.

Balagueró made his feature-length film debut with The Nameless (1999). Based on the novel by Ramsey Campbell, the film appeared at festivals worldwide, winning several awards including Best Film at the Fant-Asia Film Festival. He returned three years later with Darkness (2002). The film marked Balagueró's English-language debut, and was picked up by Miramax Studios, which released a heavily truncated version in US theaters in December 2004. 2005 saw the release of Balagueró's third film, the ghost story Fragile (2005) starring Calista Flockhart and Richard Roxburgh. Also in 2002, Balagueró co-directed the rock music documentary OT: la película (2002).

In 2006, Balagueró participated in the TV project Películas para no dormir (Films to Keep You Awake). A revival of Narciso Ibañez Serrador's macabre TV series Historias Para No Dormir (aka Tales to Keep You Awake, 1966–67 with a brief resurrection in 1982), Películas consisted of six horror-themed episodes directed by several notable horror Directors from Catalonia and other parts of Spain, including Álex de la Iglesia and Mateo Gil. Balagueró began work on REC (2007), his fourth theatrical feature, in early 2007 and planned his third movie of the REC franchise. He directed the thriller Sleep Tight, which stars Luis Tosar. Balagueró directed REC 4: Apocalypse and co-wrote along Manu Díez the screenplay, of the film. He also wrote the screenbook of REC 3: Genesis.