After being closed for a year (2016-2017) for preservation and renovation reasons, the Hypogeum is open for visitors again. Or more precisely, it's open for some visitors (80) each day. I managed to be one of those visitors in April 2019 on my trip to Malta and Sicily.
Walking up to the site through a modern neighborhood, I was wondering where the actual site was. Then I arrived at the museum, which is housed in one of those non-decrepit concrete cubicles. The cubicle does not offer any inside views, so there is little benefit to venture here without a ticket. Surprisingly, there seem to be frequent tourists, who did not get the memo and come to the museum without a ticket only to be rebuffed.
The Hypogeum tour starts with a short video, which can be booked separately. From there you get first views of the site through tinted windows. When the video was over, we descended into the underground temple. The lighting is well done and they have nice trails. The only thing to keep in mind is to mind your head as the ceiling is low.
It's a pretty large temple and taking into account how extremely old it is (3rd Millenia BCE), it's plain stunning.
Getting There
I walked from Valletta, as the site is seemingly in walking distance. But Malta is not a walking country and I would recommend simply taking the bus. Alternatively, check out taking the 3-City ferry. This will also give you an option to visit the Knights Fortifications (T) on the other side of the harbor.
But getting there really isn't the difficult part: Getting in is. The site itself is small and access is additionally restricted for preservation reasons. So plan in advance. I booked my ticket online in January for a visit in April. Price was a staggering 35€. In April, the waiting time was two months (see my picture).
If you miss out, they sell last minute tickets (40€) each morning at 9 a.m. in Valetta at the War Museum. Please check about the times and locations, as I read multiple conflicting accounts. In any case: Queue early.
If you are out of luck, you can still book the video tour. While the video is not really worthwhile, you get glimpses of the temple entry through the tinted windows.
While You Are There
When you are in the area, you should definitively visit the Tarxien, one of the Megalithic Temples. It's one of the younger temples and it doesn't offer the scenic views of the more remote temples. But it's also well preserved and accessible.