Foundational literacy is a key lever for achieving higher levels of learning and societal wellbeing. However, with an enrolment of over 250 million children in schools, India is currently challenged by learning deprivation. Growing uptake of English-medium education along with less-than-optimal English literacy instruction practices present an urgent need for improving classroom instruction. Further evidence is required on the efficacy of computer-assisted game-based learning and phonics instruction over the alphabet-spelling method in literacy learning. The current intervention study examined whether classroom phonics instruction combined with GraphoLearn, a computer-assisted reading tool, supports the English phonological awareness and reading skills better than phonics instruction alone. Participants were 6-7 year-old, Grade 2 students (N = 54) attending an English-medium public school in India. All students were non-native English speakers and received phonics instruction in their classroom for 35 min thrice a week. In addition, students were randomly allocated to play either GraphoLearn-Rime (n = 28) or a math control game (n = 26) for 15-20 min every day. Both the GraphoLearn-Rime and the math control group made significant improvement in English literacy skills over the period of intervention and the amount of exposure to phonics classroom instruction predicted gains in phonological awareness skills. The GraphoLearn-Rime group gained more than the math control group in the in-game measures. In the oral-and paper-based measures, both groups showed skill development, but the groups were not significantly different in the gains (d = 0.04 - 0.29). Overall, the study indicated the potential in the integrated approach and thus the need for more research on the effects of integrating classroom phonics instruction and GraphoLearn for supporting struggling readers of English.