Existing upper air records of radiosonde and operational satellite data recently showed a reconciliation of temperature trends but structural uncertainties remain. GPS radio occultation (RO) provides a new high-quality record, profiling the upper troposphere and lower stratosphere with stability and homogeneity. Here we show that climate trends are since recently detected by RO data, consistent with earliest detection times estimated by simulations. Based on a temperature change detection study using the RO record within 1995–2008 we found a significant cooling trend in the tropical lower stratosphere in February while in the upper troposphere an emerging warming trend is obscured by El Niño variability. The observed trends and warming/cooling contrast across the tropopause agree well with radiosonde data and basically with climate model simulations, the latter tentatively showing less contrast. The performance of the short RO record to date underpins its capability to become a climate benchmark record in the future.