The 1999 North Queensland Cowboys season was the 5th in the club's history. Coached by Tim Sheens and captained by Noel Goldthorpe, they competed in the National Rugby League.

Despite undergoing another roster clean-out in the off-season, the Cowboys endured a rough season. After starting the year with a bye, the club went on a five-game losing streak. One of the few positive periods of their season then followed, with a 24-0 win over the Auckland Warriors followed by a 20-20 draw with the Brisbane Broncos and a 20-14 win over the Balmain Tigers. The victory over the Warriors was the first time in club history that they had held a side scoreless. Following the win over Balmain in Round 9, the club won just two of their next 16 games.

The Round 25 victory over the Western Suburbs Magpies turned out to be the club's most important game of the season. Heading into the match, the Cowboys sat in 16th place, one point ahead of the bottom-placed Magpies. A loss would have more than likely seen them finish the year in last place. In Round 26, the Cowboys played the North Sydney Bears in their final ever premiership appearance. The club finished the season in 16th with just four wins, their lowest win total since 1995.

One of the players brought to the club in 1999 was former-Cronulla Sharks halfback Paul Green. In June, Green became the first Cowboys' player to represent Queensland in State of Origin. In 2014, Green returned to the club as head coach, leading them to their maiden premiership victory in 2015.

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The following players played a representative match in 1999.