Modrava was originally a settlement of fishermen. The first written record of Modrava dates back to 1614 when it is mentioned in connection with the lease of the well-fished Modravský stream. Another record occurs a year later in 1617 when the decree issued by His Majesty the King authorised free pasture at Modrava plains to those pack animals that were unable to reach Kašperské Hory on the same day. After 1757, Modrava was developing as a settlement of fishermen and hunters.
The year 1799 nevertheless brought a significant change to the location. It is when the Prince of Schwarzenberg buys from the Earl Kinský vast territory in the Prášily Estates and starts to exploit profusion of wood from local forests. The 13,6 kilometres long Vchinicko-tetovský Floating Canal was built according to the design of the engineer Josef Rosenauer in 1799-1801 as a fairway for floating logs from the Šumava forests. New directing and professional orientation of the locals also stimulated building of the Březník (Pürstling) settlement, which is the main setting of the best-known novel written by the Šumava author Karel Klostermann "From the World of Forest Seclusions".
One of the dominants of the village, the cottage of the Club of Czechoslovak Tourists called Klostermann Chalet, was built in 1924 and cost 1 041 500 Czech crowns. It was designed by the significant architect Bohuslav Fuchs. Every visitor of Modrava will also remember views of the famous Bienert Sawmill manufacturing sound boards and of the timbered building that served as a hunting lodge of the Prince of Schwarzenberg in the past.
Construction of the Czech elementary and nursery school was completed in 1934 (the building was rebuilt in 1999 to a hotel and has been serving to the new purpose ever since as Hotel Modrava).
The history of the Šumava villages is also tightly connected with smuggling. Various foodstuff as sugar, Bavarian salt, coffee, flour, or young cattle was transported through the forests of the Šumava until 1918, later also gunpowder and blasting powder. After 1784, when a state monopole prohibiting importation of the Brazilian tobacco was declared, it was mainly Bavarian snuff tobacco called "brizil" or "prizil". The smugglers were highly esteemed amongst their neighbours as their activities were not regarded as improper but as a highly beneficial work. When a farmer needed goods or commodities available at lower prices at the Bavarian side of the border, he usually addressed the closest smuggler with the request to bring them and - at the same time - gave him the goods he was supposed to take with him and transport abroad.
The circumstances occurred after the World War II, in particular the new organization of Europe and building of so-called "Iron Curtain", resulted in the extinction of the village's famous history. For instance the pub U Tetřeva na Javoří Pile, the pubs U Tří sluk and U Pstruha in Modrava and the pub Na Zlaté stezce in Filipova Huť were closed as well as the roads to Roklan and Luzný mountains. Only the memories of the old times described by Karel Klostermann remained. Certain revival of the village became after establishment of a forestry vocational school at the premises U Pstruha between 1961 and 1982.

Establishment of the Šumava National Park in 1991 represented an important historical milestone of the village's life.