In 2015, commercial surrogacy was banned in the country.
Mitsutoki Shigeta, 28, was living in Hong Kong in 2014 when he became the centre of a "baby factory" scandal, after Thai police found a plush Bangkok flat packed with infants under the care of 24-hour nannies.More news: Trump says investigation into Russia election interference is Democrats' 'excuse' for losing
The court also said Shigeta had opened bank accounts in Singapore for all 13 children whose custody he was awarded yesterday.
The man claimed he fathered the children through surrogates, and submitted DNA test results to a Bangkok court so that he could take the children back to Japan.
The ruling said Shigeta had a right to custody because the children were born before the new law was enacted, and because the surrogate mothers signed documents waiving their custody rights.More news: New raids on Syria rebel enclave kill 45 civilians
While the company's name was not cited, Japanese and Thai media have previously identified Shigeta as being the son of Yasumitsu Shigeta, the founder and chairman of Hikari Tsushin, an electronics retailer. The women delivered babies in 2014 but before Shigeta had taken them home an investigation by Interpol was launched against him, alleging he was into human trafficking.
The case of the surrogate babies came to light in 2014 when the police said they found 16 babies the man fathered with surrogate mothers in Thailand, BBC reported. The man's lawyer had said his client wanted to have dozens of babies because he desired a large family and hoped that they would inherit his fortune in the future.
Shigeta paid surrogate mothers around $10,000 each for carrying the fertilized donor eggs in their wombs. He carried out a three-year legal battle for custody, although he was not present in court on Tuesday as he left Thailand when the case emerged.More news: England beat New Zealand but miss T20 final
The man's lawyer explains his motivation for wanting so many children as "personal and business reasons".