He was accused of overstaying by three years and 10 months and faces deportation, Bangkok Post reported citing a source from the Phuket immigration police.
The police said the man was also found having cocaine and would be charged with illegal possession of drugs.
Under the current law, those who illegally possessed cocaine in Thailand may be subject to fines up to 5 million baht (US$144,317) and imprisonment from one year to life.
Overstaying for 90 days entails deportation and a ban on entering the country again.
Police said the Nigerian will be deported after legal proceedings.
Thailand, which has witnessed a strong tourism recovery since late last year, is carrying on a campaign against tourists who overstay their visas.