Haenke was born 5 October 1761 in the village of Kreibitz, Bohemia (now Chřibská, Czech Republic).
While still a student, Haenke made extensive botanical collections from what is now the Czech Republic; wrote a treatise on the botany of the Giant Mountains; edited an edition of Linnaeus' Genera Plantarum (published in 1791); and was awarded a silver medal from the Royal Czech Scientific Society.