The pair will return home after the current tour of Bangladesh with 23-year-old Kane Williamson replacing McCullum as captain in Sri Lanka where New Zealand will play three ODIs and two Twenty20s.
Left-arm seamer Boult was ruled out on Thursday of the three-match one-day series against England that started at Lord's on Friday.
Fellow pace bowler Ian Butler has replaced Boult for the England one-day series and is in line to take his place in the Champions Trophy squad.