I think that the busiest hours for arrivals are in the late afternoon. But if your flight arrives in the middle of the night you generally won't have problems - most hotels will check you in at that hour. The important thing is to contact the hotel prior to booking, inform them of the hour you plan to arrive and get confirmation that there will be no problem.
The restroom/toilet is Jerusalem bus station charges 1 shekel. There are also toilets on the top floor of MamillaMall
It is easy to find a restroom in Israel. It is a first world country. With few exceptions (some churches, bus stations) they do not charge for use..
You have 3 options before you even leave the airport (one when you are walking to passport control when you get off the plane, one in the luggage pick up area, and one in the arrivals hall just before you go out to your transportation). That gives you an idea that they are readily available in almost every tourist area and even the Old City of Jerusalem has public toilets available in the Jewish and Christian quarters. I have seen the ones at the Damascus gate and would avoid those ones but generally, you get clean (ish), modern toilets everywhere in Israel. Having taking seniors tours and teen tours to Israel, I consider myself something of an expert in this area :)
How to book a hotel... I used www.booking.com
Make sure you book into a hotel that has a 24 hour desk, and let them know your expected time of arrival when you book.
We haven't always been able to find a rest room when we want them when driving ourselves around - but McDonalds has come to our rescue on a couple of occasions. :). (And we wanted a cup of coffee anyway so bought it there).
Mostly we have found them free. We struck one the other day that charged 3 shekels.
When booking your hotel you may need to book the extra night of your arrival. So for example if you are arriving on June 1 at 5am and want a room ready, you need to book for the night of May 31st, does that make sense? since check in would be 3pm on June 1st. Definitely speak to the hotel directly about this. If you book for June 1st someone who is checking out on June 1st could be in your room when you arrive.
Petrol/gas stations nearly always have free toilets, and you don't have to buy anything there to be able to use them. Shopping malls likewise always have free toilets, and they are free in railway stations.
The flights from the US get in either early AM ( like 7 or 8) or late afternoon. I assume if you are looking at a 3AM arrival than you are coming from Europe. ( and you will be surprised how busy the airport is at that hour) I would suggest you pay for the extra night at the hotel--otherwise you will be homeless until check in time which is usually 3PM or so! ( although the hotel WILL hold your luggage when you arrive)
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