Snapchat security engineer Subhash Sankuratripati, speaking at a conference in California, said that the app had implemented the feature a year ago.
The encryption applies to "snaps" - picture and video messages sent between users, which disappear after being watched.
Other forms of message on Snapchat, such as text messages and group chats, are not end-to-end encrypted.
In the past, the company has encrypted messages, but the company held the keys that would have allowed them to be decrypted.
Although snaps disappear after being opened and were wiped from the company's servers, if users were unable to receive messages, they would be stored on the company's servers for up to 30 days.
The human rights group Amnesty International has said Snapchat's was "not protecting users' privacy".
Sankuratripati said the feature would provide "increased assurance around privacy to our users".
He added that the company planned to encrypt text and group chats in a similar way in the future.