Elon Musk estimates that a Starship launch could drop to as low as $2 million.
A Falcon 9 launch costs $50 million (when reused).
What makes such a huge price difference?
Will it use a different fuel?
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You are comparing an (estimated) cost (Starship Launch) with a price (reusable Falcon 9 launch). The actual cost of a reusable Falcon 9 launch is less than what they will charge for it-- the actual cost is known only to SpaceX, but external estimates run as low as $20 million.
The cost of the Starship launch is optimistically estimated at pretty much just the cost of the fuel/expendables. The estimate assumes that Starship/Super Heavy will fly so many times each that their amortized construction cost for a single flight is very low, and that some many Starship launches will be happening that the launch service/prep will also be inexpensive. The Falcon 9 launch cost must include the expendable second stage and the cost of the first stage amortized over only a relatively few launches. Launch prep/services for a Falcon 9 still use a pretty traditional model similar to expendable boosters, so are much more than what is envisioned for a Starship/Super Heavy, which is conceived as an everyday repetitive operation like an airport.
To sum up: the original comparison is apples to oranges; fully re-usable, very high launch cadence Starship is presumed to result in low amortized construction and operation costs, and finally the $2 million estimate is probably chock-full of Musk optimism.
The Starship launch price of $2M is very much a thought experiment.
Remember, this was announced in 2003 regarding Falcon 9 costs:
The costs, which nominally assume no advantage for recovery, are \$6M for a standard Falcon and $10M for a heavy Falcon.
With firm contract pricing set at \$12 million per flight (2003 dollars), the $1500 cost per pound to orbit will represent a new world record in the cost of access to space.
Falcon 9 is priced at \$27 million per flight with a 12 ft (3.6 m) fairing and \$35 million with a 17 ft fairing. Prices include all launch range and third party insurance costs, making Falcon 9 the most cost efficient vehicle in its class worldwide.
We went from \$6M to $60 million in quite a short time. This answer highlights a few consumer-facing prices very well.
It stands to reason that the actual launch cost of Falcon 9 is somewhere in the ballpark of \$20M for SpaceX.
Lets look at the actual quote:
"If you consider operational costs, maybe it'll be like $2 million" out of SpaceX's pocket each time, Musk said (Highlights mine)
Its a maybe and it is only talk about operational costs. this doesn't include R&D costs. And it means they are hoping to have enough launches to drive down prices. More launches means the fixed costs are divided by more launches - it also means the costs go up when they do fewer launches.