The National Weather Service was officially started in 1870 when, through a joint resolution, official weather stations were set up at military stations as part of the signal service of the War Department. In 1871 reports for stages of water and rivers were added to the stations' duties. It was believed that the weather reports were valuable enough to agriculture and commerce to warrant an appropriation bill in 1872 for storm signals to be set up at the stations. In 1890 the meteorological work of the signal service of the War Department was transferred to the Weather Bureau of the Department of Agriculture and in 1940 the Weather Bureau was transferred to the Department of Commerce. It was consolidated with the Coast and Geodetic Survey to form a new agency in the Department of Commerce called the Environmental Science Services Administration in 1965 and when the ESSA was abolished in 1970, the Weather Bureau was established within the National Oceanic and Atmospheric Administration. The name was changed back to the National Weather Service, the name it had started out with one hundred years before.

The La Crosse office of the National Weather Service was organized in 1872, and it was located in the Mons Anderson Building at 2nd and Main St. The station was relocated to the Opera House Building at 4th and Main St. in 1881 and in 1887, it moved to the McMillan Building at the NE corner of 4th and Main St. In 1890 it moved to the U.S. Court House Building at the NW corner of 4th and State St. and in 1902 it moved to the Federal Building at the NE corner of 4th & State St.

In 1907, the Weather Bureau built a building for the La Crosse Weather Station at 5th and Cass Streets. This building was used steadily by the Weather Bureau for forty-five years with one significant change; in 1943 the station lost its status as an official climatological station because of an effort by the government to "economize and eliminate duplication of work". Data was still gathered and information compiled, but it was considered unofficial. In 1952 the La Crosse station moved to offices in the administration building at the La Crosse Municipal Airport, due to the consolidation of the city and airport weather offices and the National Weather Bureau began to face the first of many federal government budget cuts. The La Crosse office, as well as others across the country, lost space, personnel and hours of operation over and over, only to gain them back again. The La Crosse office was threatened with closing many times, but the threat was never carried out. It was only moved once during this period, back to the federal building at 4th and State Streets in 1969.

Positive changes for the La Crosse office began in the late 1980s. The office was down to one employee after more federal budget cuts when it was announced that the La Crosse office had been chosen for an upgrade to a regional facility. In 1994, there was a ground breaking ceremony for a new $3 million facility including a Doppler Radar tower located on the bluff adjacent to HWY FA on the ridge east of Hixon Forest. The National Weather Service moved into the building in 1995 and staff has grown to fifteen people. The office will be adding more staff and will take over larger forecasting areas as other offices close.