Background The association between long noncoding RNAs (lncRNAs) and spontaneous regression of neuroblastoma (NB) has rarely been investigated and remains unknown. Objective To identify prognostic lncRNAs involved in the spontaneous regression of NB. Methods Differential expression analyses were performed between those samples with an outcome of death in stage 4 NB group and those samples with an outcome of survival in stage 4S NB group in two independent public datasets, respectively. Univariate Cox proportional hazard regression survival analysis was performed in each of the entire cohort to identify those lncRNAs significantly associated with overall survival (OS). Those lncRNAs independently associated with OS were then identified by multivariate Cox survival analysis and used to construct an lncRNA risk score. Results A total of 20 differentially expressed and survival-related lncRNAs were identified sharing between the two independent cohorts. The expression of each of these 20 lncRNAs was significantly correlated with the expression of NTRK1, which is a well-known factor involved in NB spontaneous regression. Four lncRNAs (LNC00839, FIRRE, LOC283177, and LOC101928100) were identified to be significantly associated with survival independent with each other and a four-lncRNA signature risk score was constructed. Patients with high lncRNA signature risk score had a significantly poorer OS and event-free survival than those with low lncRNA signature risk score. The four-lncRNA signature has a good performance in predicting survival independent with MYCN amplification (nonamplified vs amplified), age status (<18 months vs >= 18 months), risk status (low risk vs high risk), and International Neuroblastoma Staging System (INSS) stage (INSS 1/2/3/4S vs INSS 4). Conclusions We identified 20 survival-related lncRNAs that might be associated with the spontaneous regression of NB and developed a four-lncRNA signature risk score. The four-lncRNA signature is an independent prognostic factor for survival of NB patients.