Guided inquiry (GI) as a blended learning (BL) tool has a vital and significant role in the science education (Longo, 2016). Therefore, utilizing GI as a BL tool at secondary school for science education is a need of time (Shand & Farrelly, 2018). Deteriorating the quality of education in Pakistan specifically, quality of science education is needed to introduce new strategies of teaching science that can enhance learning outcomes of students, as well as teachers’ performance. For this purpose, School Education Departments are working intently with the Punjab Information Technology Board (PITB) to expand, examine, and apply the blending with classroom inquiry in public schools of Punjab. The Punjab government has arranged online books, computer labs in school, and provided tablets for both teachers and students. Consequently, secondary science teachers in government schools were using the e-learn Punjab project to practice in their classrooms. Therefore, this research was probing and explanatory to acquire a deep awareness and understanding of viability, role, experiences, and issues related to secondary science teachers regarding GI as a BL tool through coding and thematic analysis, which needed a descriptive case study. The descriptive case study was encompassed by semi-structured interviews from secondary science teachers, school principals, content developers, and classroom observation through video recording and field notes. All participants were from the public schools of Punjab where the “e-learn Punjab” project was actively working. The data revealed that secondary science teachers’ overall perception of the viability of GI as a BL tool was positive; the reason was that e-learning applications facilitated them; they were better able to deliver difficult topics or concepts, their knowledge was also updated, they had access to books in just one click, they taught with animations, and they became more active and guider. On the other hand, all the stakeholders of this study highlighted similar issues and challenges that were faced by science teachers when they used GI as a BL tool in their classrooms. Time-consuming or time management, disengagement, electricity shortage & internet connectivity, difficulty to reply during the video play, limited financial resources for maintenance, and the examination system are anti-parallels were the issues that were highlighted through findings. Based on the findings of this study, it is suggested that the government increase the financial budget allocated to schools for the maintenance of digital tools, involve various stakeholders of schools in the development of digital content, videos, and lectures, improve the e-learn project by soliciting feedback from teachers who are implementing it in their classrooms and understand the ground reality of Pakistan society to address these issues. Furthermore, relates the examination system with GI as a BL tool for better results, also include the new and updated knowledge that will facilitate the teachers to update their knowledge, as well as train the teachers regularly to improve material delivery.