Rashi (Bamidbar 1:1), says:
The Lord spoke... in the Sinai Desert... on the first of the month : Because they were dear to Him, He counted them often. When they left Egypt, He counted them (Exod. 12:37); when [many] fell because [of the sin] of the golden calf, He counted them to know the number of the survivors (Exod. 32:28); when He came to cause His Divine Presence to rest among them, He counted them. On the first of Nissan, the Mishkan was erected, and on the first of Iyar, He counted them.
This Rashi mentions 3 times the Jews were counted:
- When they left Egypt - Shemot 12:37
- After the deaths following the sin of the golden calf - see Rashi Shemot 30:16
- A month after the Shechina rested on the Mishkan, the first of Iyar. Bamidbar 1
In addition, there were other times when the Jews were counted in the desert. How many times were the Bnei Yisroel counted in the desert, and when did they happen?