The German Weather Service said the mercury hit 38.6 degrees Celsius (101.5 Fahrenheit) at 2:50 p.m. local time in Coschen, on the country's border with Poland.
The previous record stood at 38.5 Celsius (101.3 Fahrenheit), which was measured in 1947 in Bühlertal, which lies close to France.
The longevity of the previous record -- 72 years -- shows just how unusual and intense the current heat wave is in Europe. Any sign of quick relief is not on cards either.
Climate scientists have warned that heat waves such as this one are becoming more frequent and increasingly severe because of the climate crisis. Météo-France, the French national weather authority, said the frequency of such events is expected to double by 2050.
Temperatures exceeding 40 Celsius (104 Fahrenheit) are forecast in a number of major cities across the continent, with meteorologists warning that higher humidity could make it feel even hotter.
France's national weather forecaster Météo-France, increased the number of heat-related weather alerts to 78 on Wednesday from earlier 65.
A new June temperature record was also set in neighboring Poland, where meteorologists measured 38.2 Celsius.
While 100 degrees Fahrenheit might not sound like an exceptionally hot weather to some, such temperatures are far above average across central and western Europe.
"When summer temperatures are routinely in the 70s, like in northern Europe or the West Coast of the US, many places do not have air conditioning. This can turn deadly fast if heat waves strike and last for several days," CNN senior meteorologist Brandon Miller said.
National weather authorities in Belgium, the Czech Republic, France, Germany, Italy, Spain and Switzerland have issued heat warnings, advising people to avoid strenuous activities at midday and in the afternoon, drink plenty of water and stay out of the sun. Children and the elderly are particularly at risk.
Heat waves in Europe have been deadly in the past, which is why national authorities in several countries took steps to provide at least some relief to the most vulnerable people.
European public health bodies are trying to prevent a repeat of last year, when heat waves resulted in deaths in Spain and Portugal and drought conditions in Germany and Sweden.
During the record 2003 European heat wave, more than 14,000 people died in France alone.
Paris City Hall activated a plan on Tuesday that included installing 48 mist showers throughout the city, extending hours at public swimming pools, keeping some parks open all night and opening cool rooms in designated public buildings, officials said.
French national school exams also have been postponed by the education ministry, for the first time ever, to next week.
The German state of Sachsen-Anhalt has imposed a speed limit on a few stretches of the Autobahn highway system because the heat can cause road surfaces to lift.
Stephanie Halasz contributed to this story.