Prašnikar started his professional football career at his home town club Šmartno ob Paki, where he was the top scorer of the Slovenian Republic League in the 1975–76 season.
He remained in the position until December 1993, when Zdenko Verdenik took charge of the Slovenian affairs until the end of the unsuccessful qualifying campaign for the FIFA World Cup 1998.
Prašnikar was re-installed head coach in December 1997, but his second spell at the helm of Slovenia lasted for only four month as in April 1998 he resigned due to his commitments with Maribor on club-level.
Not qualified for the 2004 European Football Championship tournament, the Slovenian FA replaced Prašnikar with Branko Oblak, who was the head coach of the Slovenia under-21 at that time.
On 28 September 2007, he was appointed by Bundesliga outfit Energie Cottbus, who had parted company with head coach Petrik Sander five days earlier.