Joule heating effect is substantial in an electromagnet system due to high density current from current-carrying conductor for high magnetic field generation. In Lab-on-chip (LoC) Magnetically Activated Cell Sorting (MACS) device, Joule heating effect generating high temperature and affecting the biological cells viability is investigated. The temperature rise of the integrated system was measured using resistance temperature detector, RTD Pt100. Three temperature rise conditions which are from the bare spiral-shaped magnet wire, the combination of magnet wire and on-chip magnetic core and combination of magnet wire, on-chip magnetic core and 150 m polydimethylsiloxane (PDMS) layer have been investigated. The combination of electromagnet of spiral-shaped magnet wire coil and on-chip magnetic core has reduced the temperature significantly which are, ~ 38 % and ~ 26 % with magnet wire winding, N = 10 (IDC = 3.0 A, t = 210 s) and N = 20 (IDC = 2.5 A, t = 210 s) respectively. The reduced Joule heating effect is expected due to silicon chip of high thermal conductivity material enable fast heat dissipation to the surrounding. Therefore, the integration of electromagnet system and on-chip magnetic core has the potential to be used as part of LoC MACS system provided the optimum operating conditions are determined.