"This was the most expected 'unexpected' resignation I've ever seen," Cramer said on "Squawk on the Street." "You have flooring that was featured in '60 Minutes' and sales go down dramatically and do you give the guy a raise?"
The flooring company announced Lynch's exit Thursday morning in a release and said it was not expecting his resignation. Thomas Sullivan, Lumber Liquidators' founder, will act as interim CEO.
The company's stock fell more than 15 percent in early trading.
Lumber Liquidators' shares have been reeling ever since CBS' "60 Minutes" aired a report in March, which said the company had sold Chinese made flooring with higher levels of formaldehyde than permitted under California's health and safety standards. In response to the report, Lumber Liquidators said it stood by its products.