Kumar's arraignment in U.S. District Court in Brooklyn, New York, came a day after the company agreed to pay $225 million to past and current shareholders to settle charges that the company improperly booked $2.2 billion in revenue.
Stephen Richards, the former global head of sales for the company, also pleaded not guilty to fraud and obstruction charges.
The two former executives were charged in a 10-count indictment returned by a grand jury on Friday and unsealed Wednesday.
Kumar denied wrongdoing in a statement issued by his attorneys Wednesday and said he expects to be exonerated.
A U.S. district court judge Wednesday approved an agreement that allows the company to avoid prosecution if it pays a fine and puts a number of remedial policies in place within 18 months.
Shares of Computer Associates were up $1.67, or 6.6 percent, to $26.97 in midday trade on the New York Stock Exchange.