The average full-time salary increased by 3% to almost £24,728.
The details are contained in a report from the Northern Ireland Statistics and Research Agency.
It said 97% of staff benefited from a raise "attributable to new pay scales" that followed a review in 2011-12.
Although nearly all staff got an increase, for 35% of people the rise was between 0.1% and 1.9%.
A further 3% got no pay rise.
The average salary in the civil service compares with an average £21,345 in the private sector, according to the Department of Enterprise, Trade and Investment.
The report stated that lower-grade staff are better paid than their counterparts in the rest of the UK, though this situation is the reverse among the upper ranks.
Twenty-three staff - likely to include permanent secretaries of Stormont departments - earned more than £100,000 in 2014.
All but two of them were men.
As part of budget cuts, the NI Executive is currently exploring pay restraint and voluntary redundancies in the civil service and wider public sector.
This story was updated on 19th December to more clearly reflect the range of salary increases.
Virtually all staff in the Northern Ireland Civil Service received pay rises in 2013-2014.