Mr Whyte's lawyer entered the plea during a hearing at the High Court in Edinburgh on Thursday morning.
The 45-year-old, who lives in London, faces a charge of fraud and a second allegation under the Companies Act.
A trial is scheduled to go before judge Lady Stacey at the High Court in Glasgow in April.
The Crown has alleged that Mr Whyte fraudulently obtained a "majority and controlling stake" in the Ibrox club.
It is alleged that he directly, and through representatives, pretended to then Rangers owner Sir David Murray, and others, that funds were available to make all stipulated payments.
The second charge under the Companies Act centres on an Â£18m payment in connection with the takeover.
The former Rangers owner Craig Whyte has pleaded not guilty to two charges, including one of fraud, in relation to his purchase of the club in 2011.