Bujalski, born in Boston in 1977, is the son of artist-turned-businesswoman Sheila Dubman and businessman Edmund Bujalski. Andrew studied film at Harvard's Department of Visual and Environmental Studies where the Belgian filmmaker Chantal Akerman was his thesis advisor.

His fourth feature Computer Chess, a period film set at a computer programming tournament in 1980, premiered at the 2013 Sundance Film Festival and won the Alfred Sloan Feature Film Prize. It is his first feature edited digitally and it is the only feature film shot almost exclusively with original Sony 1968 AVC-3260 B&W video cameras.

He shot his first feature, Funny Ha Ha, in 2002 and followed it with Mutual Appreciation in 2003 – though neither film received theatrical distribution until 2005 and 2006, respectively. Bujalski wrote both screenplays and appears as an actor, playing a major role in both films. In 2006 he appeared as an actor and contributed to the screenplay of the Joe Swanberg film Hannah Takes the Stairs.

Beeswax and Computer Chess, Bujalski's third and fourth independent films, were filmed in Austin where the Director lives now. Beeswax was released in the summer of 2009. While making Beeswax Bujalski wrote a screenplay adaptation of Benjamin Kunkel's 2005 novel Indecision for Paramount Pictures.

The characters in Bujalski's films are mostly post-collegiate and middle-class; many work white collar jobs. The Desire for stability is a recurring theme, and many characters rush headlong into attempts at a more controlled existence – this is exemplified by one of the main characters in Funny Ha Ha, who elopes with his ex-girlfriend.