At the end of his university career, Fankhouser was drafted by the St. Louis Blues of the NHL and was initially sent to play for the Greenville Grrrowl in South Carolina at ECHL level, but during the season would also feature in two more leagues, the AHL and the IHL for the Louisville Panthers and the Orlando Solar Bears respectively.

During this period, Fankhouser had also moved from being under contract to the Blues to sign for the Atlanta Thrashers, and would go on to make his NHL debut for his new team featuring in 16 top-level games.

During the off-season, Fankhouser was again on the move, signing for the Reading Royals of the ECHL, but again did not complete a full season for one team, splitting his time with 19 games for the Arkansas RiverBlades.

During the summer of 2005, Fankhouser again chose to remain playing in Europe, this time for the Manchester Phoenix in the EIHL, the top level of ice hockey in Britain.

Fankhouser returned to North America and, along with Phoenix teammate Jeff MacMillan signed for the Bloomington Prairie Thunder, a team icing in the United Hockey League.