POP3 has obsoleted the earlier versions of the POP protocol, POP (informally called POP1) and POP2. In contemporary usage, the less precise term POP almost always means POP3 in the context of e-mail protocols.

The design of POP3 and its predecessors supports end users with intermittent connections (such as dial-up connections), allowing these users to retrieve e-mail when connected and then to view and manipulate the retrieved messages without needing to stay connected. Although most clients have an option to leave mail on server, e-mail clients using POP3 generally connect, retrieve all messages, store them on the user's PC as new messages, delete them from the server, and then disconnect. In contrast, the newer, more capable Internet Message Access Protocol (IMAP) supports both connected and disconnected modes of operation. E-mail clients using IMAP generally leave messages on the server until the user explicitly deletes them. This and other facets of IMAP operation allow multiple clients to access the same mailbox. Most e-mail clients support either POP3 or IMAP to retrieve messages; however, fewer ISPs support IMAP.

Clients with a leave mail on server option generally use the POP3 UIDL (Unique IDentification Listing) command. Most POP3 commands identify specific messages by their ordinal number on the mail server. This creates a problem for a client intending to leave messages on the server, since these message numbers may change from one connection to the server to another. For example if a mailbox contains five messages at last connect, and a different client then deletes message #3, the next connecting user will find the last two messages' numbers decremented by one. UIDL provides a mechanism to avoid these numbering issues. The server assigns a string of characters as a permanent and unique ID for the message. When a POP3-compatible e-mail client connects to the server, it can use the UIDL command to get the current mapping from these message IDs to the ordinal message numbers. The client can then use this mapping to determine which messages it has yet to download, which saves time when downloading.

Whether using POP3 or IMAP to retrieve messages, e-mail clients typically use the SMTP protocol to send messages. E-mail clients are commonly categorized as either POP or IMAP clients, but in both cases the clients also use SMTP. There are extensions to POP3 that allow some clients to transmit outbound mail via POP3 - these are known as "XTND XMIT" extensions. The Qualcomm qpopper and CommuniGate Pro servers and Eudora clients are examples of systems that utilize the XTND XMIT methods of authenticated client-to-server e-mail transmission.

MIME serves as the de facto standard for attachments and non-ASCII text in e-mail. Although neither POP3 nor SMTP require MIME-formatted e-mail, essentially all Internet e-mail comes MIME-formatted, so POP clients must also understand and use MIME. IMAP, by design, assumes MIME-formatted e-mail.

Like many other older Internet protocols, POP3 originally supported only an unencrypted login mechanism. Although plain text transmission of passwords in POP3 still commonly occurs, POP3 currently supports several authentication methods to provide varying levels of protection against illegitimate access to a user's e-mail. One such method, APOP (which the base specification defines as an "optional command"), uses the MD5 hash function in an attempt to avoid replay attacks and disclosure of a shared secret. Clients implementing APOP include Mozilla, Thunderbird, Eudora, and Novell Evolution. POP3 clients can also support IMAP authentication methods via the AUTH extension.

E-mail clients can encrypt POP3 traffic using SSL.

POP3 works over a TCP/IP connection using TCP on network port 110. When encapsulated in SSL, the service commonly uses TCP port 995.