Increasing complexity and applications in highly integrated system on chips (SoCs) for consumer electronics, automobile infotainments, wearables etc. the power management unit (PMU) is required to provide several power supplies efficiently for individual applications. Such multiple rails to cater to high performance in the applications involves high form factor, BOM size on chip. This paper proposes a Single-Inductor Dual-Output (SIDO) Boost converter topology with an application specific switching scheme induced with a novel control methodology to power two step-up (boost) outputs 6.3V and 5.0V from a Li-ion Battery (2.7V – 4.5V) input. The novel control scheme near almost eliminates the cross regulation amongst the outputs across all load transitions. Results show a cross regulation of 0.06 mV/mA at VOUT2 when VOUT1 is stepped up from low to rated load and 0.06 mV/mA at VOUT1 when VOUT2 is stepped up from low to rated load. Even with simultaneous maximum load transitions at both the outputs that the droops in VOUT1 and VOUT2 is 0.168 mV/mA.