Robertson attended Wichita State University and was drafted by the Florida Marlins in the fifth round of the 1999 Major League Baseball draft. Robertson underwent Tommy John surgery in 1998 while a sophomore at Wichita State. Robertson pitched for the Low-A Utica Blue Sox and Single-A Kane County Cougars; with the latter he was 6–1 with a 2.29 ERA in eight starts. Robertson returned to Kane County for the 2000 season but spent most of the year on the disabled list battling tendinitis in his left elbow. Florida moved him up to the High-A Brevard County Manatees, where he went 11–4 as a starter. Robertson’s rise continued in 2002, as Florida promoted him to the Double-A Portland Sea Dogs of the Eastern League. At Portland Robertson amassed a 10–9 record with a 3.42 ERA, sufficient that Florida summoned him to the major league club in early September.

Robertson made his Major League debut on September 7, 2002, for the Marlins, pitching 4⅔ innings and allowing four earned runs in a 4–1 loss to the Pittsburgh Pirates at PNC Park. Robertson moved to the bullpen for the remainder of the season, making five relief appearances. The following January Florida traded Robertson along with Gary Knotts and Rob Henkel to the Detroit Tigers for Mark Redman and Jerrod Fuell.

In 2005, he began wearing clear corrective lenses to correct his lazy eye.

Robertson earned his first career postseason victory on October 10, 2006, by pitching five shutout innings against the Oakland Athletics in game 1 which helped launch the Detroit Tigers into their ALCS sweep of the A’s and their first pennant since 1984.

In 2008, he tied for the major league lead in bunt hits allowed, with nine.

On August 22, 2008, Tigers manager Jim Leyland announced that Nate was being demoted to the bullpen due to ongoing trouble with his slider. Nate was quoted by the Detroit Free Press as saying that it was the “lowest point” of his career.

On March 30, 2010, Robertson was traded to the Florida Marlins for minor league pitcher Jay Voss and cash considerations. He was designated for assignment on July 21. One week later he was released.

Robertson signed a minor league contract with the St. Louis Cardinals on August 2, 2010, and was assigned to the Triple-A Memphis Redbirds. Robertson exercised an opt-out clause on August 23, and signed a minor league contract with the Philadelphia Phillies on August 24, 2010, reporting to Triple-A Lehigh Valley. On September 9, 2010, Robertson was designated for assignment by the Phillies, a day after giving up 5 runs in 2/3 innings against the Marlins and nearly blowing a 10 run lead.

On January 20, 2011, Robertson signed a minor league contract with the Seattle Mariners with an invitation to Spring training.

On February 19, 2012, the Chicago Cubs and Robertson agreed to terms to a minor league contract.

On July 14, 2012, the Toronto Blue Jays signed him to a contract. The Blue Jays assigned Robertson to their AAA affiliate Las Vegas 51s.

On January 21, 2013, the Texas Rangers signed Robertson to a minor league contract.

On March 13, 2013 Robertson signed a minor league deal with the Detroit Tigers. On May 17, 2013, Robertson was granted his release from the Tigers, as he was struggling with his command in Triple-A.

Robertson is now a pitching coach for Maize High School. In 2017, he won a state championship.