"We are a profitable company. ... We have nothing to do with this euphoric mania," Meenavalli said, later adding again that current market value the company has reached "is not a reality."

"This market cap is not justified," the company's CEO and Chairman Venkat Meenavalli said Monday on CNBC's " Fast Money ." "I valued my IPO pricing at $5."

To many, it was a textbook case of the mania surrounding digital currencies these days. Amazingly, the CEO doesn't disagree.

Shares of little-known financial technology company Longfin surged 1,342 percent in two days to a market value of $3.1 billion after buying a cryptocurrency company with no revenue.

Shares of Longfin dropped more than 18 percent in extended-hours following his comments. On Thursday, its second day as a public company, the shares closed at $5.45. On Monday, the stock closed at $72.38, giving it a $3.1 billion market value based on its current 44 million shares outstanding. (The company confirmed the shares outstanding figure with CNBC on Monday.)

The gains followed Friday's news the company was buying Ziddu.com, which says it's a microlending company using the same blockchain technology as bitcoin. Ziddu's unsecured website shows the company has a digital coin trading at 19 cents.

Longfin agreed to buy Ziddu from a private Singapore company called Meridian Enterprises in exchange for 2.5 million shares of the company. Adding confusion and volatility for investors, the filing for the deal showed Meridian is 95-percent-owned by Longfin CEO Meenavalli.

He said on CNBC that Longfin is growing at a 200 percent rate and made $28 million in the past six months. He said Ziddu "doesn't have any revenue right now" and is still in a testing phase, but he expects the subsidiary to make $3 million next year.

Blockchain technology, of which bitcoin is the first application, eliminates the need for a third-party intermediary by creating rapid, permanent transaction records. Bitcoin itself has surged more than 1,700 percent this year to above $19,000.

Other obscure, small companies have announced name changes or other new ties to blockchain, and have seen their stock surge. The pattern echoes the tech bubble of the late 1990s in which companies would add "dotcom" to the end of their names.

When asked whether he was trying to take advantage of the hype around bitcoin and blockchain, Meenavalli said, "No, not at all."

New York-based Longfin went public on the Nasdaq on Dec. 13. The company was worth $220 million in its debut of around $5 a share.

— CNBC's Tom Franck contributed to this report.