He studied medicine and natural sciences at the Universities of Vienna and Strasbourg, and in 1894 earned his medical degree, and during the following year received his doctorate of philosophy. Afterwards he worked under Carl Gussenbauer (1842-1903) at the University Hospital in Vienna and was an assistant to his father at the clinic of internal medicine. In the mid-1890s with physiologist Nathan Zuntz (1847-1920) and others, he began investigations involving physiological effects on the body associated with air pressure and altitude change, and in 1896 made the first in a series of several high-altitude balloon ascents.
In 1910 Schrötter accompanied scientists Nathan Zuntz, Arnold Durig (1872-1961) and Joseph Barcroft (1872-1947) on a expedition to Tenerife where he performed research involving respiration and oxygenation at higher elevations. During the Balkan Wars of 1912-13 he worked with the Red Cross in Montenegro, and afterwards served as a physician during World War I, which included a stint as Sanitätschef in Jerusalem. After the war he was director of Malariaspitals in Wieselburg, and following his discharge from military service, he was in charge of the Alland Lungenheilanstalt (lung hospital), which was founded by his father in 1898. In the 1920s, he made balneological studies of the Dead Sea, and in 1925 was habilitated for internal medicine at the University of Vienna.
Schrötter was a pioneer of aviation and hyperbaric medicine, and made important contributions in the study of decompression sickness. He was interested in the physiological effects that divers experienced when ascending from ocean depths, as well as the effects that higher altitudes placed upon balloonists and mountain climbers. On July 31, 1901 meteorologists Arthur Berson (1859-1942) and Reinhard Süring (1866-1950) aboard the balloon Preussen, and equipped with portable compressed oxygen containers, were able to reach 10,800 meters above sea level. However, at 10,000 meters the two scientists succumbed to unconsciousness, and from this experiment Schrötter realized that even 100% oxygen would be an insufficient safeguard against hypoxia at very high altitudes. He recognized that special pressurized breathing equipment would be necessary to maintain sufficient blood oxygenation, and proposed using a pressurized sealed chamber for very high altitude balloon flights.
Schrötter did extensive research involving pulmonary tuberculosis, and was a pioneer of bronchoscopy. In 1905 with Adolf Loewy (1862-1937), he was the first to use an endobronchial catheter as an instrument for airway separation in humans.