Pickens, who long has wanted to wean the U.S. from its reliance on foreign oil, conceded that he was a few decades early into natural gas. But he thinks its time has come.
Clean Energy's ambitious building of fueling stations has taken a toll on the company's bottom line.
And natural gas has a long way to go to dethrone oil-derived gasoline as the fuel king on the nation's freight corridors.
The vast majority of the nation's taxis, buses, shuttles and trucks still run on diesel fuel. Cleaner, low-sulfur diesel fuels and better engine technology have made diesel a strong competitor to alternative fuels for companies looking for better mileage and environmentally friendly fuels for their fleets.
And some analysts see Clean Energy as essentially a gas station chain that sells a commodity with low profit margins.
"As a fuel distributor, it's going to be exceedingly difficult for this company to be profitable on a sustained basis," said Pavel Molchanov, an energy analyst at Raymond James Financial Inc.
Analysts, though, are split over the company's prospects and recommendations on whether to buy, hold or sell the stock, which closed Friday at $11.79.
Of 11 analysts, one rated the company's stock a strong buy, and three others recommended buying it. Four analysts suggested holding the stock. Three rated it underperform or sell.
Ascendiant Capital Markets, which recommended buying shares, noted that "Clean Energy is the largest provider of natural gas fuel for transportation in North America and is leading the deployment of [natural gas] fueling infrastructure."
Analysts at Piper Jaffray reiterated a "sell" rating on shares of Clean Energy in an Oct. 8 research note to investors.
Molchanov recommended shorting the stock this year, saying the entry of other companies into the natural gas infrastructure system will put pressure on the company's chances for a profit.
A short position is essentially a bet that the share price will go down, which would result in gains for those shorting the stock.