The company was founded in 1984 under the name "JAM Software" by Andy Gavin and Jason Rubin, who were 16 years old at the time. Their first two commercial games, both developed for the Apple II, were Math Jam and Ski Crazed. Two years later, they moved up to writing software for the then next-generation Apple IIGS with the game Dream Zone, which was popular enough to be ported to several other platforms. By 1989, they wrote Keef the Thief for the Apple IIGS, and with that title, they officially changed their name to Naughty Dog. In 1991, they moved on from developing games for computers, and developed a game for the Sega Mega Drive called Rings of Power. Then, in 1995, they developed Way of the Warrior for the 3DO.
Way of the Warrior was the first game in a deal the Naughty Dog had signed with Universal Interactive Studios, which involved the creation of three additional games. These games would become the first three Crash Bandicoot titles: Crash Bandicoot in 1996, Crash Bandicoot 2: Cortex Strikes Back in 1997, and Crash Bandicoot 3: Warped in 1998. After developing the spin-off racing game Crash Team Racing in 1999, Naughty Dog left the series for good and was acquired by Sony Computer Entertainment.
After this, they developed Jak and Daxter: The Precursor Legacy for the Playstation 2 in 2001. The game received two sequels and a spin-off racing game in the forms of Jak II in 2003, Jak 3 in 2004, and Jak X: Combat Racing in 2005. They then left Jak and Daxter behind, much like they did with Crash Bandicoot.
Their next big game was Uncharted: Drake's Fortune for the Playstation 3 in 2007. They later released two more games for the series: Uncharted 2: Among Thieves in 2009, and Uncharted 3: Drake's Deception in 2011.
Their newest franchise is The Last of Us in 2013.
In July 2014, the company had announced a Naughty Dog fan art show to celebrate their 30th anniversary. The contest would include characters from their video games drawn by fans, including Jak & Daxter, Uncharted, and The Last of Us. Naughty Dog even asked Activision to included Crash fan art in the competition, but their request was denied. 
In addition, it was revealed that while there were no immediate plans to return to the Crash series, nothing would be ruled out.
As JAM Software
- Math Jam (Apple II, 1985)
- Ski Crazed (Apple II, 1986)
- Dream Zone (Apple IIGS, 1988)
As Naughty Dog
- Keef the Thief (Apple IIGS/Amiga/MS-DOS, 1989)
- Rings of Power (Genesis, 1991)
- Way of the Warrior (3DO, 1994)
- Crash Bandicoot series
- Crash Bandicoot (PS, 1996)
- Crash Bandicoot 2: Cortex Strikes Back (PS, 1997)
- Crash Bandicoot 3: Warped (PS, 1998)
- Crash Team Racing (PS, 1999)
- Jak and Daxter series
- Jak and Daxter: The Precursor Legacy (PS2, 2001)
- Jak II (PS2, 2003)
- Jak 3 (PS2, 2004)
- Jak X: Combat Racing (PS2, 2005)
- Uncharted series
- Uncharted: Drake's Fortune (PS3, 2007)
- Uncharted 2: Among Thieves (PS3, 2009)
- Uncharted 3: Drake's Deception (PS3, 2011)
- Uncharted: Golden Abyss (PS Vita, 2011) (Developed by Bend Studio, ND helped them)
- Uncharted 4: A Thief's End (PS4, 2016)
- Uncharted: The Lost Legacy (PS4, 2017)
- The Last of Us series
- The Last of Us (PS3, 2013)
- The Last of Us Part II (PS4, 2018-19 upcoming)