He turned professional later that year, immediately after winning a place on the European Tour at final qualifying school.

He followed up a consistent Challenge Tour season with success at qualifying school to return to the top level for 2001.

He managed to retain his European Tour card by finishing inside the top 100 on the Order of Merit in both 2001 and 2002, but his form dipped in 2003 and he dropped back down to the second tier for 2004.

After a slow start to the season, he recorded back to back second-place finishes, before rounding off the season with victory in the Kazakhstan Open and another runners-up prize at the Apulia San Domenico Grand Final.

Challenge Tour playoff record (0–1) Note: Pilkington only played in The Open Championship.