The 16-year-old Plymouth College pupil had won a bronze in the 100m butterfly event on Friday.
She was back in the pool on Saturday morning and progressed through the heats and semis to reach the 50m butterfly final.
Stephens swam her best time of the day in the final, clocking 27.49 seconds, but she had to settle for sixth place in a fast race won by Russian Polina Egorova in 26.82.
Austria’s Caroline Pilhatsch was second in 27.18 and Denmark’s Julie Jensen third in 27.19.
There was disappointment for fellow Plymouth Leander swimmer Tom Fannon.
The Plymouth College pupil failed to reach the men’s 50m freestyle final – an event where he was ranked fastest on paper going into the Games.
Fannon had clocked a stunning time of 22.48 seconds at the British Championships – a national age group record – but he could only manage 23.03 in the semi-finals in Baku. That was quicker than his 23.26 heat swim but was not fast enough to reach the final.
Had he been able to reproduce his British Championship time on Saturday then he would have won a silver medal.
Meanwhile, Leander’s Joe Hulme, who had narrowly missed out on two medals in the 100m and 200m backstroke events, helped Great Britain reach the men’s 4x100m medley final, where they won silver.
Hulme swam in the heats, but was replaced in the final by junior world record holder Luke Greenback. However, having featured in the qualifying round, Hulme was awarded a medal.
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