Clean Environment and Stable Energy Market Act of 2009

Clean Environment and Stable Energy Market Act of 2009 - Amends the Internal Revenue Code to require covered persons (i.e., coal producers, oil refinery operators, and producers and importers of other greenhouse gases emission substances) to purchase a federal emission permit (denominated in carbon dioxide equivalents) from the Secretary of the Treasury for the sale or use of a greenhouse gas (GHG) emission substance. Exempts from such requirement GHG emission substances to be used: (1) as material in the production of another article by such person; or (2) for noncombustion agricultural purposes. Requires the Secretary to impose a GHG emission permit equivalency fee on imports of carbon intensive goods.

Requires the Secretary, after consultation with the Administrator of the Environmental Protection Agency (EPA) and the Secretary of Energy, to establish a price for obtaining a permit for a year based on a determination of the dollar amount necessary to ensure that the demand for permits does not exceed the GHG emission allocations for such year. Requires the Secretary to publish a five-year price schedule for permits by January 1, 2010, and every five years thereafter. Authorizes the Secretary to modify the schedule.

Sets forth a formula to determine the national GHG emission allocation limitations for 2011-2050.

Provides for refunds of permit fees to specified: (1) permittees that use GHG emission substances in a manner that will make a negligible or no contribution to global warming; and (2) exporters of carbon-intensive goods.

Imposes a tax on covered persons who fail to obtain a required permit.

Establishes in the Treasury the Climate Protection and Economic Security Trust Fund where revenue raised from permit sales shall be deposited.

Applies this Act to the sale of any GHG emission substance after December 31, 2010.