The manuscript presents the design and development of a Microwave Hyperthermia (MHT) applicator integrated with an Electromagnetic (EM) lens. The purpose of the proposed MHT applicator is to provide non-invasive microwave hyperthermia treatment for skin cancer. The proposed MHT applicator comprises of an EM lens (133.75 × 133.75 mm3) placed ahead of a Hybrid Fractal Microstrip Patch Antenna (HFMA) (30 × 26 × 1.645 mm3), backed by a Meshedgrid-shaped Artificial magnetic Conductor (AMC) (48 × 48 × 3.27 mm3) reflector at an optimal distance of 16 mm The prototype of the HFMA is fabricated on a Rogers (RT5880) substrate and offers an impedance BW of 278 MHz, for a frequency from 2.316 to 2.594 GHz. To improve the front-to-back ratio (FBR) of the proposed HFMA, an EM lens that reduces the beam width and concentrated the energy in the desired direction is integrated with the AMC-backed HFMA. The final MHT applicator configuration provides a 3 dB beam width of 49.6° and a gain of 7.35 dBi at 2.45 GHz. The testing and validation of the proposed MHT applicator is carried out in a simulation environment using Computer Simulation Technology (CST) Multiphysics for thermal analysis to check the temperature rise in the phantom. An in-vitro sample of skin phantom with a tumor is prepared using chemicals mimicking skin properties is exposed to the EM radiations emitted by the proposed HT applicator excited using a RF signal generator and power amplifier. the temperature rise in the phantom is recorded using optical temperature measurement probe. A temperature rise in the cancer-affected area up to 44 °C (Effective Temperature Area (ETA) 36 × 20 mm2) is observed in the simulation environment for an exposure time of approx. 45 min and in the measurement environment after a span of 25 minuites. A reported Specific Absorption Rate (SAR) value of 10 W/Kg shows that the proposed MHT applicator is safe for human exposure, and also reduces hot spots by enhancing the focus with controlled temperature, thus making the proposed applicator safe for human exposure.