Originally, Winpopup was a very basic communication utility from Microsoft, packaged with Windows 95. This little tool was used as a sample implementation to Microsoft Winpopup protocol that could be used to send short instant messages between the users on the same LAN. The protocol survived through the time and multiple versions of Microsoft operating systems, the latest implementation being the Messenger service on Windows XP. However, today this service causes much more headaches than it brings benefits. Malicious users and Internet advertisers exploited the Winpopup protocol to send spam advertising, causing loss of productivity in organisations because of multiple pop-up windows appearing on the users' computers. Current security advisories recommend stopping and disabling Messenger service to prevent pop-up flooding.

Winpopup LAN Messenger was initially thought of as an advanced messaging tool that would be compatible with Microsoft Winpopup. However, due to inherent flaws in the Microsoft Winpopup communication protocol, Winpopup LAN Messenger has deliberately ceased compatibility with the original Winpopup.

Currently, Winpopup LAN Messenger uses secure proprietary protocol that works over TCP/IP. TCP/IP has multiple benefits over the standard Winpopup, being inherently more secure, reliable, and transparent to routers and corporate firewalls. Microsoft Winpopup, on the other hand, uses the old NetBIOS protocol that has multiple flaws, such as lack of any security and vulnerability to flooding by malicious users.

Winpopup has two modes for its graphical user interface. One mode resembles most common messengers such as ICQ or MSN Messenger. The other mode adds some advanced features, such as group broadcasting and conferencing, not found in other messengers.