Background and Objectives: Early detection of dental caries lesions at active stages of development can facilitate their monitoring and reduce needs for restorative dental care. This study aimed to describe the prevalence and caries treatment needs in first permanent molars of pre-school children, based on a caries lesion activity assessment, and in relation to participants’ ages, dental plaque levels and toothbrushing habits. Materials and Methods: Large cross-sectional dental caries survey using multistage cluster sampling was conducted among Lithuanian 4–6-year-old children attending kindergartens. For the present study purpose, all individuals presenting erupted permanent molars were selected. Thus, only 5–6-year-olds (n = 453) took part in this study. They were examined for caries by one calibrated examiner using Nyvad clinical diagnostic criteria that differentiate between active and inactive caries lesions. Dental plaque was assessed by the Silness-Löe index, and parents’ reports about toothbrushing frequency were collected. Results: Overall, 41% of permanent molars were affected by caries; 6-year-olds had more caries lesions than 5-year-olds (p < 0.05). Mean number of decayed and filled surfaces (DF-S) of all participants was 1.79 (SD 2.93), half of lesions were noncavitated, more than one-third were cavitated and fillings comprised less than one surface per child. Majority of lesions were active; prevalence of inactive lesions (all noncavitated) was 1% and 6% in 5- and 6-year-olds, respectively. Prevalence of active lesions increased with age; it correlated with plaque levels and with toothbrushing frequency (<0.001). Likelihood to detect active lesions was up to nine times higher in teeth with abundant plaque (odds ratio (OR) 8.73; confidence interval (CI) 5.35–14.25), and up to seven times higher in individuals brushing teeth irregularly (OR 6.88; CI 2.21–21.41). Conclusions: The obtained data indicate high treatment needs in the erupted permanent molars of the Lithuanian pre-school population and imply that caries management should primarily focus on improved biofilm removal, accompanied with regular use of fluoridated toothpaste.