Once upon a December, I tried to go to the California Academy of Sciences the week after Christmas. That story didn’t have a a fairytale ending: we didn’t get in, the scene outside the Academy was wicked, so we headed to some quieter places in Golden Gate Park. But I was determined to take my son for a visit, so we made a second attempt this last summer. This time, we came prepared with my plan of attack, and we had a great time. With only one trip under my sleeve, I am not an expert, but I did gain a few insights that I can pass on to you.
1. Buy your tickets online. On very crowded days, the Academy will stop selling tickets soon after it opens. Pre-purchase tickets to save yourself from the disappointment of being turned away or the possibility of standing in another line to purchase them there.
2. Queue up early. I don’t need to tell you that the early bird gets the worm. There will be a line at the entrance before the museum opens. You need to be in that line, so that you can be one of the first groups to get inside and enjoy some of the exhibits before it gets unbearably crowded.
3. Get your tickets for the shows as soon as you walk in. From the entrance, go left to the planetarium and snatch your tickets. You can choose which show time you prefer, so you don’t necessarily have to go to the first show. You will want to see the aquarium or the rainforest exhibit early, so opt for a later showtime. We were not able to see the 3-D Bug Show, but they do sell out of those tickets early as well.
4. The fishes don’t mind the crowds, but you might. After you get your tickets, head directly to the Steinhart aquarium. It is dark in that section and the design makes the crowds seem even more unbearable. This is the section where you want to especially hold on to your toddlers so that they don’t get lost. I know you want to enjoy some quality time with the jellyfish and not the museum security, so go to the aquarium early.
5. Ready, set, go: Rainforest. The rainforest exhibit opens an hour after the museum, and although museum employees discourage people from queueing up too early, people do anyway. For us, this was the highlight of the museum, so I don’t recommend you skip this. The butterflies are the main attraction, and they are more plentiful in the higher levels of the dome. They will land on you, so don’t go if you get queasy about insects. My son stood there for about ten minutes, waiting for the butterflies to land on him. One finally did. 
6. Bring your own lunch and seat. The meals are pricey and the dining areas are small. It’s common to see families eating their lunch on the floor of the Academy Cafe. We bought a snack, and had a bigger meal outside the museum afterwards.
7. The penguins are as crowded as the people gawking at them. After you hit the three main areas, head over to Africa Hall for a stroll through a very quiet African savannah. This is the retro part of the museum and the home of the penguins. They are cute, even I’ll admit it.
8. Take a breath on the Living Roof. If you need a break, go up to the trademark plant-covered roof. It is a lesson in green design and offers some good views of the plaza. 



I went over the summer but totally wish I had these tips prior to my visit. I agree on the aquarium that the layout is tight. We enjoyed our time, but never got to the main attractions because of the exact reasons you mention. Now I’m inspired to go again!
You forgot 9) Wait a couple of years until the newness wears off and the crowds die down. We were members and I still never made it to the rainforest or planetarium because of crowds at any time or day of the week.
I really need to plan for West Coast trips especially San Francisco. Did I tell you how much I love SF?
Love the plant roof, how neat!!!
Meg, you’re right I do need to add the disclaimer for #9. I may have to update the post ending. On another day, when I’m not suffering from a case of Tuesday-itis.
Hey, I’m so glad you posted these tips! Our first year membership at the new digs is about to expire and I can’t believe I still haven’t posted anything about it. You are right it’s crazy busy there still. Amazing.
I agree on all points! Good tips.
Here is my tip- Go on a really rainy day. We went a couple weeks after it reopened and waited for crappy weather and it totally worked. It wasn’t really crowded at all and we had a great time.