There are no 'corporate' owned car hire businesses in the Amtrak Jacksonville, (JAX) Florida station. However, as with many transport locations across the US, the car-hire companies service the Amtrak passengers.
With Hertz, Avis, and Budget, once you have an advanced reservation that indicates you're arriving via Amtrak, they will instruct you to first phone their local number, advising them that you have arrived. They will then either instruct you to take a taxi to their designated office where you will sign your rental agreement and collect your vehicle. You will be asked to obtain a receipt from the taxi driver and you will be reimbursed either in cash, or in most cases, the taxi cost will be applied to your rental agreement as a credit to your final bill.
In some instances, the car-hire company may arrange to collect you and take you back to their offices. Because the Amtrak station is not located in downtown Jacksonville, this is generally not the case.
Many of the tertiary hire companies will not compensate for transport to their offices.
For car-hire bookings involving non-airport locations, it's always advisable to consider dealing directly with the car-hire company, rather than the plethora of on-line booking engines as many of them make an automatic presumption that the car hire will commence and terminate in an airport.
Finally, as a caveat; Generally, Corporate owned locations, such as Hertz, Avis, Budget, in Jacksonville airport will have far lower prices than say arranging a booking through a franchise location. As an example, a local hotel, country club, or garage may be listed as a rental location. However, the pricing structure is based upon having no competition at that location. Consequently, your rental contract price will be much higher. Additionally, your choice of vehicle may be quite limited to the most basic mid-line type of vehicle.
It may be advisable, before finalising your booking, to weigh up the value-v-inconvenience of getting yourself to the airport to collect your vehicle. Unfortunately, Jacksonville International Airport is quite far from downtown Jacksonville.
As a final thought; Florida is considered a 'pool' state, whereby vehicles may be collected and dropped of anywhere within the state. The collection point will determine the overall price: Daily/Weekly rate + CDW, CDW, PAI, etc. But there will be no additional charge for a pre-arranged returned to a specific location.
This does not apply to a car-hire that is being taken out of state.
Be aware that Florida rental rates are exclusive to the state. If you plan to take the vehicle out of state (Jacksonville is just a few miles from the Georgia State line), ensure you have pre-arranged this with your hire company. Otherwise you may be shocked to discover that your original agreed price has dramatically changed when you come to settle up, as your taking the car across the state line invalidates the agreement. (continual GPS monitors are covertly fitted in All hire cars in Florida). There exists promotional rates that allow tourists to visit such beautiful locations as Savannah, Sea Island, (The Cloister), and Hilton Head. (South Caroline).
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