Scientific reasoning represents a set of skills students need to acquire in order to successfully participate in scientific practices. Hence, educational research has focused on developing and validating assessments of student learning that capture the two different components of the construct, namely formal and informal reasoning. In this opinion paper, we explain why we believe that it is time for a new era of scientific reasoning assessments that bring these components together, and how computer-based assessments (CBAs) might accomplish this. Reasoning is a mental process that enables people to construct new representations from existing knowledge (Rips, 2004). It includes cognitive processing that is directed at finding solutions to problems by drawing conclusions based on logical rules or rational procedures (Mayer and Wittrock, 2006). When people reason, they attempt to go “beyond the information given” to create a new representation that is assumed to be true (Bruner, 1957). The process of scientific reasoning comprises formal and informal reasoning (Galotti, 1989; Kuhn, 1993). Formal reasoning is characterized by rules of logic and mathematics, with fixed and unchanging premises (Perkins et al., 1991; Sadler, 2004). It encompasses the ability to formulate a problem, design scientific investigations, evaluate experimental outcomes, and make causal inferences in order to form and modify theories related to the phenomenon under investigation (Zimmerman, 2007). Formal scientific reasoning can be applied not only within the context of science, but in almost every other domain of society (Han, 2013). It can be used to make informed decisions regarding everyday life problems (Amsterlaw, 2006); for example, individuals use proportional reasoning to decide the fastest way to travel from one place to another. In informal reasoning, students draw inferences from uncertain premises as they ponder ill-structured, open-ended, and debatable problems without definitive solutions (Kuhn, 1991). When students reason formally, they work with the given premises in belief mode, which concerns arriving at true and warranted conclusions whereas informal reasoning is carried out in design mode, which focuses on identifying relevant premises that can be used to establish a strong argument (Bereiter and Scardamalia, 2006). Since a premise of informal reasoning is uncertain and can be questioned, its conclusion can be withdrawn in the light of new evidence (Evans, 2005). This process involves weighing the pros and cons of a particular decision (Voss et al., 1991). Learners engage in informal reasoning when they deal with socio-scientific issues—controversial issues that are influenced by social norms and conceptually related to science, such as whether or not to consume genetically modified food or support government's plan for a car-free city (Sadler and Zeidler, 2005). Both types of reasoning are used to manipulate existing information and share the same goal of generating new knowledge. While formal reasoning is judged by whether or not conclusions are valid, informal reasoning is assessed based on the quality of premises and their potential for strengthening conclusions. The manipulation of existing information in formal and informal reasoning processes can be described with dual-process theories of reasoning (Evans, 2007; Glockner and Witteman, 2010). According to these theories, there are two distinct processing modes: Type 1 processes are autonomous and intuitive processes that do not heavily rely on individuals' working memory, whereas Type 2 processes involve using mental simulation or thought experiments to support hypothetical thinking and reflective processes that require working memory (Evans and Stanovich, 2013). An individual's first response to a problem tends to be processed automatically and refers to their past experiences and personal beliefs (i.e., Type 1 process: Evans, 2008). For example, when using formal reasoning to decide the fastest way to travel from A to B, an individual's first thought might be to take a plane since it is commonly considered the fastest means of transport. However, the individual might change his or her mind after processing all necessary information, such as the travel time to and from the airport. Not every individual is able to progress after the first stage and produce a rational decision. Those who are confined to Type 1 processes make intuitive decisions, whereas more experienced individuals utilize Type 2 processes to construct a well-informed choice (Wu and Tsai, 2011). In the example of using informal reasoning to decide whether or not to support a government's plan for a car-free city, intuitive thought might lead individuals to support the plan based on their experiences with pollution. However, with the purpose of generating new representations, only those who can (a) elaborate on their intuitive decision with acceptable justifications; (b) address opposite arguments; and (c) think about how the plan can be further improved are utilizing Type 2 processes. In this regard, there is a strong connection between formal and informal reasoning, in which both types of reasoning share the common goal of generating new knowledge by processing available information through the dual stages. Activity in belief mode covers a broad range of scientific practices in school science (Bereiter and Scardamalia, 2006). Outside the classroom, however, students need to make decisions regarding problems with uncertain premises by working in design mode. Teachers should have ways to assess how students improve on their existing ideas by searching beyond what they already know rather than simply making sure their ideas align with accepted theories. It is therefore important to build a scientific reasoning assessment that incorporates both formal and informal reasoning skills in order to better measure the constructs underlying scientific reasoning. In the following, we argue that these complex skills can be best assessed using computer-based testing.