An infusion pump system and method with common line auto flush, wherein the infusion pump system has a first reservoir, a second reservoir, a junction, a common line having one end in fluid connection with the junction and having a terminal fluid delivery end, and an infusion pump. The method includes infusing the first fluid at a first rate along a first flow path; entering a common line flush volume value for the common line; switching from the first flow path to a second flow path; driving the second fluid at the first rate along the second flow path; monitoring volume of the second fluid driven at the first rate; and driving the second fluid at a second rate along the second flow path when the monitored volume is equal to or greater than the common line flush volume value.