Yes, several times.
The most famous one is Mt.Gox. Japan-based Bitcoin exchange Mt. Gox had been operating since 2010 and was the biggest Bitcoin exchange at the time.
But very few know that this big exchange was not hacked only once, but twice.
The first one happened in June 2011 when the hacker was able to get ahold of Mt.Gox’s auditor’s credentials and transferred 2609 bitcoins to an address for which Mt. Gox had no keys. This led to the suspension of Mt. Gox operations for several days; but they sustained themselves in the market, and they were able to regain the trust of users.
Here's a big article about it.
https://coinsutra.com/biggest-bitcoin-hacks/