The board said in a statement after a meeting on Friday that it believes the probe commission was "properly constituted in accordance with the IPL operational rules" and will thus approach the Supreme Court.
The Bombay High Court declared the panel "illegal and unconstitutional" on Tuesday as it was not formed in line with the BCCI's own rules.
The BCCI's two-member panel, comprising former judges Jayaram Chouta and R. Balasubramanian, cleared Chennai Super Kings team principal Gurunath Meiyappan and Rajasthan Royals co-owner Raj Kundra of betting and keeping in touch with illegal bookmakers.