Khan was accused with seven others of killing a gazelle and two protected antelopes in Rajasthan in 1998.
Khan, 50, is one of Bollywood's biggest stars, appearing in more than 80 films.
Last month Khan created an uproar when he told reporters that work on his latest Bollywood film was so gruelling that he felt like a "raped woman".
The actor had challenged a verdict by a lower court that convicted and sentenced him to one and five years in jail respectively for the two cases of poaching.
High Court Judge Nirmaljit Kaur cleared Khan in both cases, ruling that the pellets recovered from the animals were not fired from his gun.
"The honourable high court has not agreed to the prosecution evidence or its documents in both the cases. Definitely, it's a good thing that an innocent man has received justice," the actor's lawyer Hastimal Saraswat told NDTV news channel.
The actor was not present for the ruling.
He was charged with killing two black bucks, a protected antelope species, during a hunting trip in 1998.
The original case was filed by the local Bishnoi community, who revere and worship the black bucks.
Last year Khan was acquitted after being charged with running over and killing a homeless man in a driving accident. The government has challenged his acquittal in the Supreme Court.
A court in India has acquitted Bollywood star Salman Khan of shooting and killing endangered animals two decades ago.