Monex's shares spiked 20 percent following the announcement, as of 11:35 a.m. HK/SIN.
Monex, Japan's No.3 online brokerage by customer accounts, said in a statement it would execute the deal on April 16. Coincheck's CEO and COO will resign from the board of directors and become the company's executive directors, Monex said.
Coincheck was hit by a daring $530 million theft of digital money earlier this year, prompting penalties from Japan's financial regulators for lax security protocols.
Toshihiko Katsuya, Monex's managing director and senior executive officer, will become president and representative director of Coincheck.
The deal will allow Monex to access Coincheck's trading platform and customer base. Monex said Coincheck generated net income of 471 million yen ($4.4 million) for the year ended in March.
The deal bring another mainstream financial services operator into the frontier cryptocurrency trading market in Japan. Larger rival SBI Holdings last year obtained a licence to run a cryptocurrency exchange, but in February postponed plans to do so as it sought to bolster the security of its exchange.