I have received a bunch of questions about this one. So here’s a quick write-up about how to cross the southern-most Jordan-to-Israel land border.
If you’re arriving from Petra (Wadi Musa), you’ll probably go to the bus station in downtown Aqaba. While you can ask to be let out at the turnoff to the airport, the bus station is your best bet to catch the cab you’ll need to reach the border.
Walking or hitchhiking aren’t serious options. Because the access route to the border crossing is a few kilometers from any other road, you can only hope to hitch one of the few cars that are also heading to Israel.
The charge from the bus station to the border is about JOD10. Note, that if you’re going the other way (Israel to Jordan), there are usually no cabs waiting at the border. You have to get lucky, or you ask one of the border guards to make a call for you (expect to have little haggle room and pay more than JOD10).
In the season, you might be able to carpool from Wadi Musa (Petra) or Wadi Rum with other tourists. But off-season there are simply not enough people crossing.
I had to unpack my backpack at a checkpoint about a kilometer before the actual border and then had another check at the actual border.
From the bag check, I went to the third in a line of windows. I showed my passport and received my leaving stamp (if you have your visa stamp on a separate paper you’ll be handing it in here), and then had to go to window #7 for another stamp.
When I arrived at the final gate from Jordan to Israel, the guard sent me back to window #7. I didn’t have a receipt for my JOD10 departure tax. The guy at window #7 should have taken my money.
So I turned back to him.
After going back and forth three times the two finally communicated with each other. They determined that window #7 guy was correct: I didn’t have to pay because I had stayed in Jordan long enough and had entered over land.
On the Israeli side, I had to unpack my backpack again. While two people were having a look at the contents of my bags, I was questioned for about ten minutes by a stern-looking lady. She was quite interested in the Sudan stamp in my passport and the length of my travels. But eventually, she was satisfied with my explanations.
After this and considering that I had only been out of Israel for two weeks, I wasn’t sure what kind of visa I would get. It turned out that there was nothing to worry about: I received a brand new visa giving me the full three months to roam around Isreal.
While packing up, I got to chat with the only other two people — a German-English couple –crossing with me, and we agreed to share a taxi into Eilat. We were lucky, as one just pulled in to drop off a Russian couple as we came out into the parking lot. NIS50 shared between three is bearable for the 15-minute drive.
The other option is to walk the ca. 1km up to the main road and wait for a bus into Eilat (or towards Be’er Sheva and Jerusalem). Apart from Friday afternoon and most of Saturday, buses pass about hourly. Note, however, that during peak season Jerusalem-bound buses might be full. It Is advisable to book a ticket in advance.