Average and Range. According to an average of salaries from jobs listed on Indeed, the average church secretary makes about $28,000 per year. Salary Expert lists salaries ranging from the low $30,000s to the mid $40,000s.The Bureau of Labor Statistics reports an average for all secretaries of $35,330 per year.It's important to note, however, that many churches employ secretaries on a part-time basis, often for only a few hours each week.alary Expert lists salaries ranging from the low $30,000s to the mid $40,000s. The Bureau of Labor Statistics reports an average for all secretaries of $35,330 per year. It's important to note, however, that many churches employ secretaries on a part-time basis, often for only a few hours each week.