Those gaining A* to C grades in English rose from 68.8% to 73%, Maths rose 1.6% to 66.2% and Science from 61.5% to 64.8%.
Overall, the number of pupils achieving A* to C grades increased by 1.5% to 78%.
While more boys achieved A* to C grades than last year, girls continued to outperform them by 7.6%.
By Maggie TaggartBBC News NI Education Correspondent
Northern Ireland boards test pupils in sections or modules.
Old-style O levels and, from 1986, GCSEs were offered as linear exams, with a single test at the end of two years study.
In 2009, modular style exams were introduced in GCSEs across the curriculum.
They split the course of study into sections or "modules" and each one is tested throughout the two years.
A previous education secretary for England, Michael Gove, decided to change that.
He used two arguments: he wanted to reduce the amount of testing pupils had to cope with and he also thought the linear exam would be more "robust".
Not everyone agrees and some argue that pupils can actually get better results from linear testing.
In Northern Ireland, Education Minister John O'Dowd decided not to follow suit and the exams offered by the CCEA, the Council for the Curriculum, Examinations and Assessment, have retained the option of modular exams.
Performance by students in Northern Ireland in individual sciences was particularly high, the Joint Council for Qualifications said.
The proportion of entries awarded A* to C in Biology sits at 93.3% (91.2% in 2013), in Chemistry 93.6% (93.4% in 2013) and in Physics 95.0% (94.7% % in 2013).
The overall improvement comes despite concerns about changes to the style of test taken by English examination boards.
In English Language, Northern Ireland improved while in Great Britain the results have worsened. The English-based boards dropped the 'speaking and listening' element of the exam, but it was retained by Northern Ireland.
The Joint Council for Qualifications said there were notable performances in Music and modern languages:
CCEA director of qualifications Anne Marie Duffy said the results reflected the hard work of students and teachers.
"The performance in core subjects of English and Mathematics will provide strong foundations for learners as they move on to further education, training and employment," she said.
"This year there has been a 2.8% points fall in the Northern Ireland Year 12 school population, and we've seen GCSE entries decrease by 3,609.
"Against this backdrop, entries in Business Studies and ICT have risen while sciences and modern languages have maintained their popularity."
Careers' information can be found at www.nidirect.gov.uk/results or, you can call 0300 200 7820.
For those with queries on any issues relating to their exam results, for example appeals, remarks or re-sits, contact your exam centre or the CCEA helpline on 028 9026 1260 or email helpline@ccea.org.uk.
GCSE pupils in Northern Ireland have shown improvements in English, Maths and Science.