In Uppsala Forsskål was one of the students of Linnaeus, but apparently also studied with the orientalist Carl Aurivillius, whose contacts with the Göttingen orientalist Johann David Michaelis are probably the reason why Forsskål travelled to the University of Göttingen in 1753; he studied Oriental languages and Philosophy and completed a doctorate there with a dissertation entitled Dubia de principiis philosophiae recentioris (1756).

On Michaelis's recommendation, and with Linnaeus's approval, Forsskål the next year (1760) was appointed by Frederick V of Denmark to join, amongst others, the orientalist and mathematician Carsten Niebuhr on an expedition to Arabia.

Just 31 years old, Forsskål worked hard on collecting botanical and zoological specimens, but fell ill with malaria and died in July 1763.

The entire journey of this Danish expedition was the subject of Thorkild Hansen's first book, Det lykkelige Arabien (1962, translated into English as Arabia Felix).

Forsskål's companion Niebuhr, who was the only one of the participants to survive the expedition, was entrusted with the care of editing his manuscripts, and published in 1775 Descriptiones Animalium – Avium, amphiborum, insectorum, vermium quæ in itinere orientali observavit Petrus Forskål.

In the same year his account of the plants of Yemen and of lower Egypt also appeared, under the title of Flora Ægyptiaco-Arabica sive descriptiones plantarum quas per Ægyptum Inferiorem et Arabiam felicem detexit, illustravit Petrus Forskål.

Most of his specimens were lost in transport or deteriorated due to bad storage in Copenhagen; his herbarium was reconstructed some 150 years after his death by the botanist Carl Christensen.

In subsequent botanical works many different variants of his name were recorded (Forsskål, Forskål, Forskåhl, Forsskåhl, Forsskaal, Forskal, Forsskal, occasionally also Forsskaol).