Two men have been charged after one of them allegedly attacked a quokka, while the other filmed it, on Western Australia's Rottnest Island.

Police allege about one of the men kicked the small marsupial several times before chasing it about 6pm yesterday.

The other man allegedly uploaded the video to social media.

Video obtained by 9NEWS showed an unidentified man chasing the small marsupial around a residence.

Officers caught the men, aged 20 and 21, as they were leaving the island today.

The quokka has not been found and it is unclear if it was injured.

The men have been charged with cruelty to animals and will face Fremantle Magistrates Court on March 13.