The bespectacled Wong, 19, famed for his galvanising role in the city's 2014 pro-democracy "umbrella movement", was held upon arrival at Bangkok's Suvarnabhumi airport late Tuesday.
After obfuscation from Thai officials over the activist's whereabouts, his political party -- Demosisto -- issued a statement on Wednesday afternoon confirming Wong had been put on a flight back to Hong Kong.
The party, co-founded by Wong this year, also said it "strongly condemns the Thai government for unreasonably limiting Wong's freedom and right to entry."
Speculation swirled that Thailand's military government was acting under pressure from regional superpower China -- a key ally who has lavished investment and diplomatic support on a junta lacking international friends following its 2014 coup.
Thai student activist Netiwit Chotipatpaisal, who invited Wong to speak in Thailand, said police had told him of a "written letter from the Chinese government to the Thai government concerning this person".
Junta spokesman Colonel Winthai Suvaree said he was unaware of any formal request from Beijing, while an airport immigration official confirmed there had been an "order" to detain Wong but declined to say who issued it.
Netiwit later led a few dozen students wielding umbrellas -- in a nod to Wong's movement in Hong Kong -- in a protest at a Bangkok campus, shouting "Joshua Wong has the right to be here."
Wong has been a perennial thorn in Beijing's side since emerging as an unlikely leader of protests against Chinese political domination of the city.
His supporters initially expressed concern that Wong could be sent to mainland China, like a Hong Kong book seller critical of Beijing who was detained in Thailand last year while on holiday.
Thailand's China kowtow
Last year Wong was similarly barred from entering Malaysia, where officials sent him back to Hong Kong citing fears his planned talks would damage ties with Beijing.
The Thai military has also busily suppressed its own student pro-democracy protests since its 2014 power grab.
But it would not be the first time the kingdom's junta has appeared to act under pressure from China.
"The Thai military government has kowtowed to China in the past, to Thailand's own detriment," said Thitinan Pongsudhirak, a politics expert at Chulalongkorn University.
He cited Bangkok's deportation of more than 100 Uighurs who had fled China in 2015, a move that drew widespread condemnation from rights groups who say the Muslim minority are heavily repressed by Beijing.
Weeks later a bomb in the Thai capital killed 20 people, mostly ethnic Chinese tourists, in an attack many experts link to Thailand's treatment of the Uighurs -- a claim Thai authorities refute.
Deporting Wong will "be counterproductive because it will attract global attention," Thitinan said, adding it will "send a signal that Thailand's space is not open".
Wong had been due to speak at an event in Bangkok on Thursday marking the 40th anniversary of a massacre of pro-democracy students by security forces and royalist militias.
The Thammasat massacre of October 6, 1976, remains a deeply sensitive issue in Thailand's recent history.
Wong's detention also comes almost a year after Hong Kong bookseller Gui Minhai disappeared in Thailand.
He later resurfaced in China, one of a number of men detained by Chinese authorities over their involvement in the selling of titles critical of Beijing's leaders.
Wong was among three student leaders convicted in August over the 2014 storming of the forecourt of Hong Kong government headquarters, an event that preceded mass protests that brought much of the city to a standstill for months.
His party Demosisto wants a referendum on Hong Kong's future, including the option of independence.
