The original Native name for Haines was Deishú, meaning "end of the trail" by the Chilkat group of Tlingit. It received this name because they could portage (carry) their canoes from the trail they used to trade with the interior, which began at the outlet of the Chilkat River, to Dtehshuh and save 20 miles (32 km) of rowing around the Chilkat Peninsula.

The sudden importance of the region increased the urgency of fixing an exact boundary. There were reports that the U.S. harassed Canadian citizens as a deterrent to making any land claims. In 1898 the national governments agreed on a compromise, but the government of British Columbia rejected it. U.S. President McKinley proposed a permanent port lease near Haines, but Canada rejected that compromise.
The economy continued to grow and diversify. Four canneries were constructed around the mission by 1900. However, the completion of the White Pass and Yukon Route railway in neighboring Skagway that same year led to the Dalton Trail's eventual abandonment and Haines' economic decline.

All but one of the canneries had closed by 1972 due to declining fish stocks, thus leaving Haines Packing Co. as the sole remaining cannery presently located in Haines. Nonetheless, commercial fishing remains an integral part of the local economy. Logging and sawing timber has been an industry around Haines but has declined also in recent years. In October 2002, voters approved a measure consolidating the city of Haines and Haines Borough into a home-rule borough.