No, you cannot fly anywhere with marijuana. Commercial airports and airlines are under Federal jurisdiction. Marijuana remains illegal under Federal law and the TSA does not respect local law. Where you are flying does not matter as the marijuana becomes illegal as soon as you enter a commercial airport. The TSA may just warn you, but they also could prosecute you.
In general, the answer is no. Under federal law marijuana is an illegal Schedule 1 narcotic deemed to have a “high potential for abuse and no medical value.” The federal law doesn’t distinguish between medical marijuana and recreational marijuana – any form of the substance is illegal. Since airports, airspace, and airplanes all fall under federal jurisdiction, anyone found flying with medical marijuana is at risk of being detained, arrested, and prosecuted under federal law.
However, TSAs official policy has stated they are not specifically looking for marijuana and if they do happen to find it in a routine search, it’s largely up to the individual TSA agent to decide how to respond. In states where medical marijuana is legal, anecdotal evidence suggests local police will often verify a passenger’s documents and allow them to fly with medicinal cannabis if everything is in order.
Federal law states that you can never fly with marijuana, even if it is medically prescribed. Flying instate does not matter, it is against the law. All airports and planes are under federal jurisdiction, anyway. TSA rarely, if ever, searches for drugs, though. So, it may be worth the risk to hide it well in your travels.