n 1996, in Charlottesville, Virginia, friends of Darius Van Arman who performed in a band under the moniker The Curious Digit had just recorded a new album, but they were signed to no label. They had previously released a 7″ record on the short-lived label Sentimental, which was co-run by Van Arman and a friend Dawson Prater (who later went on to eventually start the Locust Music label out of Chicago). Sentimental, however, became inactive when Prater moved away from Charlottesville. Working under the theory that having some sort of label-affiliation would be better for The Curious Digit than if they self-released the album, Van Arman started Jagjaguwar.

Initially, The Curious Digit album Bombay Aloo was going to be the only album released on Jagjaguwar, but a Richmond band called Drunk performed at the venue Tokyo Rose where Van Arman booked musical acts. Mesmerized by their performance, Van Arman persuaded Drunk to release their new record, which the band had just completed, through Jagjaguwar.

In 1999, Chris Swanson, who was part owner of the record label Secretly Canadian, became partners with Van Arman and Jagjaguwar and Secretly Canadian became much more tightly connected, sharing office space and some staff. Most recently, the other two partners of Secretly Canadian, Ben Swanson and Jonathan Cargill, became equal partners of Jagjaguwar as well, although, A&R-wise, Chris Swanson and Van Arman solely decide what is released on Jagjaguwar. In February, 2007, the partners behind Secretly Canadian and Jagjaguwar, along with Phil Waldorf, former label manager of Misra Records, announced a third sister label, Dead Oceans. The three labels share offices and staff in Bloomington, IN.

The name Jagjaguwar was generated using a Dungeons & Dragons character name-generating program