Traveling from Israel to Jordan via the Wadi Araba border crossing in 2016
Jordanian government seems to have changed the visa rules starting 01 January, 2016. They no longer let you get visa on arrival at Wadi Araba border crossing (Eilat / Aqaba). The internet forums are full of people who are lost and have no idea what to do. The official advice is to get a visa from the embassy in advance, though this is not always possible / cost effective. There is pretty much no information online on what to do if you’re unable to get a visa from the embassy.
There is a solution though, they’ll let you enter Jordan if you have a Jordan Pass. Jordan pass includes the visa fee as well as entrance to Petra and other tourist places, so it really saves you a lot money and time. Sending your passport to the embassy and getting a visa is much more expensive. So, just get the Jordan pass, have your passport, arrive at the border crossing, pay the Israeli exit fee and you’re in Jordan :) I am not sure if this is valid for all countries, but it worked with Lithuanian passports, so it should be the same for all EU citizens.
P.S be sure to read the conditions of Jordan Pass. If you want to get your visa fee waived, you need to spend at least 3 nights in Jordan.
This information is based on my own experience when crossing from Eilat to Aqaba on January 14th, 2016. I am not to be held accountable if your experience is different.
If there are any questions, feel free to email me at: firstname.lastname@example.org