Background: Prior research has indicated that high levels of motivation and subjective well-being can predict engagement in challenging academic situations and achievement. Yet studies in the field have yielded inconsistent results in young elementary school students indicating a need to further examine this topic. This is particularly urgent for young children during the foundational years of early elementary school when they are learning critical academic skills including reading. Method: We examined the relationships between reading motivation, school-based well-being as covitality, and literacy achievement in 268 second graders in the process of reading acquisition in Hebrew. Well-being and reading motivation were examined by questionnaires designed and/or adapted for young elementary school students and literacy skills by language and reading tests. Results: Findings showed a positive correlation between reading motivation and full-scale covitality scores, as well as most of its first order factors (gratitude, optimism, zest and persistence). Furthermore, both reading motivation and covitality were positively correlated to reading skills and language abilities. Significant differences were found between students with low-medium reading motivation and those with high motivation in all covitality subfactors and most literacy measures, in favour of children with high reading motivation. Conclusions: The worrisome picture, that children with low reading motivation also report low levels of covitality, suggests that proper attention should be paid throughout first grade to both reading motivation and school-based well-being, both of which might affect learning. Because children's cognitive readiness is related to their socioemotional well-being, children with poor language abilities and emergent literacy skills may require special support to prevent their expected reading difficulties and the negative emotions attached to them. Thus, designing reading instruction programmes that implement motivational aspects should be a high priority interest for educators that teach young children.