The best replacement for secretary is administrative assistant.

The best alternatives to secretary are rated as following:
★★★★★  administrative assistant
★★★★  paralegal
★★  assistant
★★  receptionist
★★  treasurer
★  legal assistant
★  minister
★  personal assistant
★  clerk
★  boss
  executive assistant
  secretariat
  recording secretary
  corresponding secretary
  secretary
  office assistant
  undersecretary
  treasury
  under secretary
  50 shades of grey
  director
  admin

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Speaking about secretary, one probably shouldn't forget about boss.

Other search terms related to secretary and their ratings are:
★★★★★ boss
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secretary
administrative assistant
paralegal