Pekka Niskanen began his clarinet studies at the Puolalanmäki Music Classes under Esko Parikka. During his conservatory studies, his teachers included Seppo Salovaara and Tapio Liukkonen. Later, he continued at the Sibelius Academy, where he was guided by Harri Mäki and Kari Kriikku. In 2000, he started working with the Lapland Chamber Orchestra, which provided practical experience as a musician and also influenced the progress of his studies. He graduated with a Master of Music degree in 2008.

Niskanen has participated in numerous masterclasses led by, among others, Anna-Maija Korsimaa, Romain Guyot, Alan Hacker, Andrew Marriner, Charles Neidich, and Wenzel Fuchs. He has performed as a chamber musician both in Finland and abroad, and has appeared with ensembles such as the Tampere Philharmonic Orchestra, Turku Philharmonic Orchestra, Finnish National Opera Orchestra, and the Avanti! Chamber Orchestra.