The organization of the language network undergoes continuous changes during development as children learn to understand sentences. In the present study, functional magnetic resonance imaging and behavioral measures were utilized to investigate functional activation and functional connectivity (FC) in three-year-old (3yo) and six-year-old (6yo) children during sentence comprehension. Transitive German sentences varying the word order (subject-initial and object-initial) with case marking were presented auditorily. We selected children who were capable of processing the subject-initial sentences above chance level accuracy from each age group to ensure that we were tapping real comprehension. Both age groups showed a main effect of word order in the left posterior superior temporal gyrus (pSTG), with greater activation for object-initial compared to subject-initial sentences. However, age differences were observed in the FC between left pSTG and the left inferior frontal gyrus (IFG). The 6yo group showed stronger FC between the left pSTG and Brodmann area (BA) 44 of the left IFG compared to the 3yo group. For the 3yo group, in turn, the FC between left pSTG and left BA 45 was stronger than with left BA 44. Our study demonstrates that while task-related activation was comparable, the small behavioral differences between age groups were reflected in the underlying functional organization revealing the ongoing development of the neural language network.