SMP Negeri 4 Pakem was founded in 1952. When it was first established, this school was named SMP Pancasila. Year after year, this school changed its name, once it was given the name SMP PANCASILA, SMP PAEDAGOGIK, SMP FIP III IKIP, SMP PERCOBAAN 2, SMP PERCOBAAN 3, SDL IKIP, and in 1977, precisely on May 20, it became SMP Negeri 3 IKIP Yogyakarta. This junior high school was originally a private school and then became part of UGM, which is based in the Faculty of Pedagogy. Following the establishment of IKIP Yogyakarta, this school became the parent of IKIP Yogyakarta.
In 1987, the Directorate General of Higher Education transferred this school under the auspices of the DIY Regional Office, Directorate General of Primary and Secondary Education. The name of the school became SMP N 2 PAKEM. Since then, this school, together with other state junior high schools, has been within the DIY Regional Office of the Department of Education and Culture.
Since taking shelter at the DIY Regional Office, managerially, institutionally, and the educational and teaching processes of this school have relatively needed to adapt and this has taken a relatively long time. This is due to previous habits, almost every program and policy was only in the form of a program package and the school was the complete implementer. For example, a continuous advanced module system has been implemented, the initial concept of which was very good, but in its implementation teachers and students were bound by the fact that knowledge was only limited to modules. Modules as the only learning resource. With this habit, coupled with very underdeveloped infrastructure, this school has relatively limited space for movement. Starting in 1994, the school originally had two groups per group with a total of 20 students per group, The capacity has been increased to three groups per generation. This school graduated three rombel (classes) for the first time in 1997.
In 1997, the name of this school was changed to SLTPN 4 Pakem. The nomenclature with the number 4 is because this school is included in the regional office of the Ministry of Education and Culture in fourth place.
In 1999 there was a change of principal, from Drs. Marsum to Mrs Woro Triwulan Ambarwati, BA The new school principal has been provided with adequate management training. However, at the beginning it was not able to provide significant changes due to the old habits of this institution. One year later they started to form an Academic Quality Improvement (PMA) team (Chaired by Mr. Ponidi, who at that time had been at this school for 2 years). Even though there are various obstacles, especially psychological obstacles because they are considered very junior, the PMA team continues to improve. This team continues to be supported by the school principal so that it continues to move and is able to mobilize other components, especially in the academic field. Academic achievement continued to move from 9th place in 1999 to 3rd place in 2003.
Tahun 2003, saat pemerintah gencar dengan Manajemen Peningkatan Mutu Berbasis Sekolah (MPMBS), Sekolah ini ditetapkan sebagai sekolah masih relatif terbelakang, tetapi memiliki potensi sehingga diberikan Bantuan Operasinal Manajemen Mutu (BOMM). Dengan BOMM, tim sekolah yang diketuai Pak Ponidi memilih prioritas tiga program strategis, yaitu penguatan ICT, Penguatan KIR, dan Penguatan Bahasa inggris. Tentu semua program ini dapat berjalan dengan keputusan kepala sekolah. Waktu itu sekolah belum memiliki komputer. Ibu Woro Triwulan Ambarwati, selaku kepala sekolah, merelakan 10 komputer pribadinya digunakan untuk kursus. Walau saat itu dengan operasi under dos yang tertinggal dengan sekolah lain yang sudah menggunakan windows, siswa-siswi sangat antusias.
Tahun 2004, Pemerintah melaunching program Sekolah Standar Nasional (SSN). Walapun Standar Nasional belum ada, tetapi semangat pemerintah dan sekolah sangat luar biasa. SMPN 4 Pakem ditetapkan sebagai SSN. Saat itu dari 3 SMP SSN di Kabupaten Sleman, SMPN 4 Pakem belum yang terbaik, tetapi semangat semua warga untuk menjadi yang terbaik sangat tinggi. Tiga program strategis tetap menjadi unggulan saat SSN. Tiga tahun kemudian, SMPN 4 Pakem bisa menjadi SSN terbaik di Kabupaten Sleman. Bahkan, capaian UN waktu itu dapat menjadi peringkat 2 di DIY.
Tahun 2007, seiring dengan program pemerintah, sebagai SSN terbaik di Kabupaten Sleman, SMPN 4 Pakem ditetapkan sebagai Rintisan Sekolah Bertarap Internasional (RSBI). Sepanjang menjadi RSBI mengalami pasang surut pencapaian akademik.
Tahun 2013, Program RSBI dibubarkan. Pada saat itu terjadi euforia “wis ora RSBI”. Semangat sangat turun. Demikian pula untuk kelas (rombel) yang semula rombel kecil berjumlah 4 atau (sebenarnya 3 rombel standar) ditambah menjadi 5 rombel standar. Dengan kata lain, menambah 2 rombel tiap angkatan, sama dengan tahun 1987 ketika sekolah ini alih posisi dari Dikti ke Dikmenum. Saat RSBI bubar, sekolah ini banyak mengalami kendala baik berupa pendanaan, beban mengajar, maupun raw input siswa. Ibarat seorang anak yang tadinya banyak menyusu ibu dalam hal ini kepada kementerian, saat itu dilepas begitu saja seolah jadi anak nakal.
Akhir 2013, kepala sekolah purna. Selanjutnya awal 2014, Pak Ponidi yang saat itu telah lebih dari 2 tahun bertugas di sekolah lain ditarik kembali ke SMP 4 Pakem. Kini Pak Ponidi hadir bukan sebagai guru saja, tetapi sebagai kepala sekolah. Dalam suasasana yang sangat berat, dengan beban yang lebih berat, semua warga SMPN 4 Pakem bersatu bertekad “RSBI boleh bubar, tetapi virus mutu harus terus mengakar dan menyebar”.
Up to 3 years (2016) it still felt difficult, but with continued enthusiasm, SMPN 4 Pakem was finally able to continue to achieve the best academic performance. Starting from 2017 until this article was written in May 2021, achievements in various things ranging from arts, sports, religion, technology, character, even management and innovation, this school is very proud of. Not only does it make the residents of SMPN Pakem proud, but it makes all the residents of Sleman and DIY proud.