Nadeem Anjarwalla, a British-Kenyan dual national, was arrested in February with his US colleague Tigran Gambaryan.
Their detention came as the Nigerian authorities investigated alleged wrongdoing by Binance.
The company has not commented on the accusations it has been facing.
“We were made aware that Nadeem is no longer in Nigerian custody. Our primary focus remains on the safety of our employees and we are working collaboratively with Nigerian authorities to quickly resolve this issue,” a Binance spokesperson said.
Mr Anjarwalla, the company’s Africa regional manager, and Tigran Gambaryan, in charge of financial crime compliance at the firm, were arrested on 26 February after attending meetings in Nigeria’s capital, Abuja, to which they had been invited by the government, Binance said.
The authorities reportedly demanded that they name Nigerians trading on their platform.
A court granted the Economic and Financial Crimes Commission’s request to detain the two executives for 14 days, but their continued detention was not authorised by the court, a source close to the families told the BBC.
They were due to appear again in court on 4 April.
Nigerian media are reporting that Mr Anjarwalla asked the guards at a guest house where he was being held to allow him to go to the mosque last Friday but never returned.
The authorities had reportedly confiscated his British passport but the whereabouts of his Kenyan passport was unknown.
“Nadeem left Nigeria by lawful means,” the source close to the families said. Mr Gambaryan remains in custody.
Meanwhile, the Nigerian authorities have formally filed tax evasion charges against Binance at the High Court in Abuja, and named Mr Anjarwalla among the respondents.
The Federal Inland Revenue Service is accusing the cryptocurrency platform of non-payment of value added tax, company income tax, failure to file tax returns and complicity in aiding customers to evade taxes through its platform.
Last month, the Nigerian authorities clamped down on cryptocurrency firms in general over allegations they were being used for money laundering and financing terrorism.
The country’s central bank alleged that over $26bn (£20.6bn) worth of transactions had passed through Binance with untraceable sources.
It accused the platforms of fixing exchange rates and currency speculation leading to the free-fall of the naira, the local currency, and ordered the firm to pay a fine of $10bn.
Binance is understood to be one of the most popular cryptocurrency platforms in Nigeria.
Africa’s largest economy is battling an economic crisis worsened by the weakening of the naira, the soaring cost of living, and food inflation.