Tyler and Cameron Winklevoss announced Gemini in June 2013, and the company went live on October 25, 2015. Gemini began to facilitate the purchase and storage of Bitcoin through a complex system of private keys and password-protected environments. Gemini holds a Limited Purpose Trust Charter from the New York Department of Financial Services that was granted in October 2015. Subsequently, Gemini began adding to the financial services it offers, some of which include FIX and API support.

On May 5, 2016, Governor Andrew Cuomo of New York State announced the approval of Gemini as the first licensed Ethereum exchange based in the United States. In 2016, Gemini announced it would allow users to withdraw Ethereum Classic (ETC) from the exchange, following a hard fork in Ethereum's code.

In April 2018, Gemini began offering "Block Trading." Block Trading enables Gemini users to buy and sell large quantities of digital assets outside of Gemini's continuous order books, creating an additional liquidity mechanism when trading in greater size. Also in April, Gemini began utilizing NASDAQ's SMARTS technology to monitor trades and combat fraudulent activity and price manipulation on its exchange.

On May 14, 2018, the New York Department of Financial Services announced it had approved Gemini to offer Zcash (ZEC) on its platform, becoming the first licensed exchange to offer trading and custody services. On September 10, 2018, Gemini received regulatory approval for a new product, the Gemini dollar (GUSD), from the NYDFS and would launch trading of the coin that same day. Gemini described the product as a stablecoin that maintains a 1-to-1 peg with the American dollar. On October 3, 2018, it was announced that Gemini had obtained digital asset insurance covering tokens and coins held on its exchange. The insurance had been brokered by Aon, a London-based public risk consulting company, and underwritten by a consortium of global underwriters.

In May 2023, Gemini announced that Dublin, Ireland, would be the location for the company’s headquarters in Europe. In January 2024, Gemini received crypto registration in France, allowing the company to provide service in the country.