Both actual motor competencies (AMC) and perceived motor competencies (PMC) play an important role in motor development research and children's physical and psychological development. PMC refer to children's perceptions of their motor competencies. To assess the PMC of first and second grade children (aged 6–9 years), the SEMOK-1-2 instrument was developed. The instrument is aligned to the validated MOBAK-1-2 instrument which assesses AMC in the competence areas “object movement” and “self-movement” Accounting for possible reading difficulties in younger children, the motor tasks and answer options were illustrated and explained verbally. The purpose of this study was to test and validate the SEMOK-1-2 instrument and investigate the associations between the constructs AMC, PMC and physical activity (PA), whereby PA was measured by the participation in team and individual sports. Data from N = 404 pupils in the German-speaking part of Switzerland from first and second grades (M = 7.8 years, SD = 0.69, 49% boys) were analyzed. Confirmatory factor analyses were conducted to test the factorial validity of the SEMOK-1-2 instrument. Structural equation models were used to investigate the association between the constructs. The analyses confirmed a two-factor structure with the factors PMC “object movement” and PMC “self-movement”, corresponding to the factors existing in the MOBAK-1-2 instrument. Latent correlations between AMC factors and the corresponding PMC factors were r = 0.79 for “object movement” and r = 0.76 for “self-movement”. Associations with external criteria and covariates, such as sex, were associated with both AMC and PMC. Analyses also revealed that children who participated more often in individual and team sports showed higher levels in both AMC and PMC. The confirmation of the two-factorial structure of the SEMOK-1-2 instrument and the associations between AMC and PMC as well as external criteria indicate construct and criterion validity. The SEMOK-1-2 instrument can be economically utilized for assessing PMC and is also suitable for the monitoring of PMC in the context of Physical Education.