The iPhone maker's stock has lost roughly 14 percent in the last 12 months as Wall Street soured on its prospects amid reports of iPhone production hiccups. CNBC reported Monday that, among analysts, Apple's stock is the most "unloved" it has been since 2005.
"In terms of the naysayer, I've heard this over and over again," Cook said in an exclusive interview with Jim Cramer. "I've heard it in 2001, I've heard it in 2005, in '7, in '8, in '10, in '12 and '13. You can probably find the same quotes from the same people over and over again."
"I'm not defensive on it. This is America and you can say what you want," Cook continued. "But ... my honest opinion is that there is a culture of innovation in Apple and that culture of innovation combined with these incredible, loyal customers, happy customers, this ecosystem, this virtuous ecosystem, is something that is probably underappreciated."
Last week, Apple lowered its fiscal first-quarter guidance in a letter to investors, citing a weakening economy in China and softer-than-expected iPhone sales as partial reasons for the revision. The letter, attributed to Cook, also said lower-than-anticipated iPhone upgrades stemmed from fewer carrier subsidies, a stronger U.S. dollar and cheaper battery replacements.
Shares of Apple plunged on the report as investors fretted that the weakness in China could lead to boycotts of Apple products, a claim Cook has disputed as anecdotal.
"I'm never surprised by the market, to be honest with you, because I think the market is quite emotional in the short term," Cook said when asked about Wall Street's reaction to the news. "We sort of look through all of that. We think about the long term. And so when I look at the long-term health of the company, it has never been better. The product pipeline has never been better. The ecosystem has never been stronger. The services are on a tear."
Cook highlighted Apple's large installed user base, which hit 1.3 billion one year ago and has added 100 million users in the last 12 months, and the under-the-radar success of the iPhone XR, which he said has been "the most popular iPhone ... every single day from when we started shipping until now."
In the Tuesday interview, Cook also said he was "very optimistic" when asked about the prospects for U.S.-China trade talks.
Apple shares rose on Tuesday, closing up 1.91 percent at $150.75. The company will officially report fiscal first-quarter earnings Feb. 7.
Disclosure: Cramer's charitable trust owns shares of Apple.