After playing in the 2004 Claxton Shield he made his professional debut in the US minor leagues, with the GCL Phillies.

He led the Gulf Coast League in innings, tied Luis Valdez for the win lead, was three strikeouts behind leader Gabriel Sosa and was second to Gaby Hernandez in ERA.

In 2006, Scott was a more refined 1–1 with a 1.12 ERA for the Perth Heat in the 2006 Claxton Shield after having sat out the 2005 tournament.

That winter, he was traded to the Oakland Athletics in the minor league portion of the Rule 5 draft.

In his first year in Oakland, Scott pitched for the Kane County Cougars (5–3, 1.74) and the Stockton Ports (1–0, 1.69).